bioroebe 0.12.24 → 0.13.31

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Files changed (503) hide show
  1. checksums.yaml +4 -4
  2. data/LICENSE.md +7 -8
  3. data/README.md +566 -354
  4. data/bin/all_positions_of_this_nucleotide +1 -1
  5. data/bin/aminoacid_frequencies +1 -1
  6. data/bin/automatically_rename_this_fasta_file +1 -1
  7. data/bin/base_composition +1 -1
  8. data/bin/batch_create_windows_executables +1 -1
  9. data/bin/bioroebe +12 -1
  10. data/bin/bioroebe_cat +7 -0
  11. data/bin/calculate_exponential_growth +7 -0
  12. data/bin/calculate_n50_value +1 -1
  13. data/bin/calculate_the_frequencies_of_this_species +7 -0
  14. data/bin/chunked_display +1 -1
  15. data/bin/codon_frequency +1 -1
  16. data/bin/codon_to_aminoacid +1 -1
  17. data/bin/colourize_this_fasta_sequence +1 -1
  18. data/bin/complementary_dna_strand +1 -1
  19. data/bin/complementary_rna_strand +1 -1
  20. data/bin/consensus_sequence +1 -1
  21. data/bin/dna_to_rna +1 -1
  22. data/bin/downcase_chunked_display +1 -1
  23. data/bin/download_this_pdb +1 -1
  24. data/bin/fasta_index +1 -1
  25. data/bin/fetch_data_from_uniprot +1 -1
  26. data/bin/filter_away_invalid_nucleotides +1 -1
  27. data/bin/find_substring +1 -1
  28. data/bin/input_as_dna +1 -1
  29. data/bin/is_palindrome +1 -1
  30. data/bin/leading_five_prime +1 -1
  31. data/bin/longest_ORF +1 -1
  32. data/bin/longest_substring +1 -1
  33. data/bin/open_reading_frames +1 -1
  34. data/bin/partner_nucleotide +1 -1
  35. data/bin/plain_palindrome +1 -1
  36. data/bin/random_dna_sequence +1 -1
  37. data/bin/random_sequence +1 -1
  38. data/bin/raw_hamming_distance +1 -1
  39. data/bin/return_longest_substring_via_LCS_algorithm +1 -1
  40. data/bin/reverse_sequence +1 -1
  41. data/bin/short_aminoacid_letter_from_long_aminoacid_name +1 -1
  42. data/bin/show_atomic_composition +1 -1
  43. data/bin/show_fasta_header +1 -1
  44. data/bin/show_nucleotide_sequence +1 -1
  45. data/bin/show_this_dna_sequence +1 -1
  46. data/bin/show_time_now +7 -0
  47. data/bin/sort_aminoacid_based_on_its_hydrophobicity +1 -1
  48. data/bin/strict_filter_away_invalid_aminoacids +1 -1
  49. data/{lib/bioroebe/base/reset.rb → bin/three_delimiter} +9 -6
  50. data/bin/three_to_one +1 -1
  51. data/bin/to_rna +1 -1
  52. data/bin/trailing_three_prime +1 -1
  53. data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +1 -1
  54. data/bioroebe.gemspec +6 -7
  55. data/doc/README.gen +534 -322
  56. data/doc/blosum/blosum.md +4 -0
  57. data/doc/compatibility/BIO_PHP.md +20 -18
  58. data/doc/compatibility/README.md +2 -3
  59. data/doc/compatibility/emboss.md +5 -3
  60. data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md} +4 -2
  61. data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md} +36 -33
  62. data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md} +3 -3
  63. data/doc/statistics/statistics.md +12 -10
  64. data/doc/todo/bioroebe_GUI_todo.md +6 -1
  65. data/doc/todo/bioroebe_java_todo.md +3 -2
  66. data/doc/todo/bioroebe_todo.md +328 -310
  67. data/doc/{using_biomart.md → using_biomart/using_biomart.md} +7 -3
  68. data/lib/bioroebe/abstract/features.rb +0 -0
  69. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -1
  70. data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +3 -1
  71. data/lib/bioroebe/aminoacids/codon_percentage.rb +18 -10
  72. data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +5 -2
  73. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +90 -64
  74. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -3
  75. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +2 -2
  76. data/lib/bioroebe/annotations/create_annotation_format.rb +2 -2
  77. data/lib/bioroebe/base/base.rb +101 -6
  78. data/lib/bioroebe/base/base_module/base_module.rb +9 -1
  79. data/lib/bioroebe/base/colours.rb +3 -0
  80. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +80 -44
  81. data/lib/bioroebe/base/commandline_application/README.md +1 -1
  82. data/lib/bioroebe/base/commandline_application/commandline_application.rb +661 -22
  83. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +2 -1
  84. data/lib/bioroebe/base/infer_the_namespace_module/infer_the_namespace_module.rb +37 -0
  85. data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +1 -6
  86. data/lib/bioroebe/base/prototype/prototype.rb +155 -14
  87. data/lib/bioroebe/biomart/attribute.rb +1 -1
  88. data/lib/bioroebe/biomart/biomart.rb +8 -9
  89. data/lib/bioroebe/biomart/server.rb +1 -1
  90. data/lib/bioroebe/blosum/blosum.rb +2 -2
  91. data/lib/bioroebe/calculate/calculate_blosum_score.rb +5 -3
  92. data/lib/bioroebe/calculate/calculate_gc_content.rb +1 -1
  93. data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +5 -3
  94. data/lib/bioroebe/calculate/calculate_melting_temperature.rb +2 -10
  95. data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +6 -15
  96. data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +4 -2
  97. data/lib/bioroebe/cell/cell.rb +3 -2
  98. data/lib/bioroebe/cell/specialized_cells/B_cell.rb +60 -0
  99. data/lib/bioroebe/cell/specialized_cells/Macrophage.rb +60 -0
  100. data/lib/bioroebe/cell/specialized_cells/README.md +5 -0
  101. data/lib/bioroebe/cell/specialized_cells/T_cell.rb +60 -0
  102. data/lib/bioroebe/cleave_and_digest/cleave.rb +3 -1
  103. data/lib/bioroebe/cleave_and_digest/digestion.rb +1 -1
  104. data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml +93 -0
  105. data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml +72 -0
  106. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -2
  107. data/lib/bioroebe/codons/codon_table.rb +10 -2
  108. data/lib/bioroebe/codons/codons.rb +3 -3
  109. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +18 -15
  110. data/lib/bioroebe/codons/determine_optimal_codons.rb +1 -1
  111. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +4 -2
  112. data/lib/bioroebe/codons/show_codon_tables.rb +1 -1
  113. data/lib/bioroebe/codons/show_codon_usage.rb +1 -2
  114. data/lib/bioroebe/codons/show_this_codon_table.rb +2 -2
  115. data/lib/bioroebe/codons/start_codons.rb +7 -3
  116. data/lib/bioroebe/colours/colour_schemes/README.md +1 -1
  117. data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +3 -3
  118. data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +3 -3
  119. data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +4 -3
  120. data/lib/bioroebe/colours/colour_schemes/helix.rb +3 -1
  121. data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +3 -1
  122. data/lib/bioroebe/colours/colour_schemes/score.rb +13 -2
  123. data/lib/bioroebe/colours/colour_schemes/strand.rb +3 -1
  124. data/lib/bioroebe/colours/colour_schemes/turn.rb +3 -1
  125. data/lib/bioroebe/colours/colour_schemes/zappo.rb +1 -1
  126. data/lib/bioroebe/{toplevel_methods/colourize_related_methods.rb → colours/colourize_related_code.rb} +1 -3
  127. data/lib/bioroebe/colours/colourize_sequence.rb +3 -1
  128. data/lib/bioroebe/colours/colours.rb +172 -15
  129. data/lib/bioroebe/configuration/configuration.rb +1 -1
  130. data/lib/bioroebe/constants/GUIs.rb +2 -2
  131. data/lib/bioroebe/constants/constants.rb +1349 -0
  132. data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +8 -13
  133. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +9 -3
  134. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +11 -10
  135. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +1 -1
  136. data/lib/bioroebe/count/count_at.rb +2 -1
  137. data/lib/bioroebe/databases/download_taxonomy_database.rb +1 -1
  138. data/lib/bioroebe/dotplots/advanced_dotplot.rb +2 -2
  139. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +2 -2
  140. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +2 -2
  141. data/lib/bioroebe/electron_microscopy/flipy.rb +2 -2
  142. data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +3 -11
  143. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +6 -6
  144. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +6 -6
  145. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +2 -2
  146. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +1 -1
  147. data/lib/bioroebe/enzymes/restriction_enzyme.rb +1 -1
  148. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +4 -3
  149. data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +1 -1
  150. data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +4 -3
  151. data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +3 -3
  152. data/lib/bioroebe/ext/main.cpp +0 -1
  153. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +3 -3
  154. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +1 -1
  155. data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +1 -1
  156. data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +8 -14
  157. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -1
  158. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +1 -1
  159. data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +1 -1
  160. data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +1 -1
  161. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +37 -11
  162. data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +2 -2
  163. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +1 -1
  164. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +5 -13
  165. data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +1 -1
  166. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -1
  167. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +3 -6
  168. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +3 -3
  169. data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +20 -11
  170. data/lib/bioroebe/genome/genome.rb +1 -1
  171. data/lib/bioroebe/genomes/genome_pattern.rb +17 -16
  172. data/lib/bioroebe/genomes/genome_retriever.rb +4 -2
  173. data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +10 -13
  174. data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb +557 -0
  175. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/aminoacid_composition.rb +498 -198
  176. data/lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb +665 -0
  177. data/lib/bioroebe/gui/universal_widgets/blosum_matrix_viewer/blosum_matrix_viewer.rb +329 -0
  178. data/lib/bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +423 -0
  179. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/controller/controller.rb +170 -118
  180. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +277 -215
  181. data/lib/bioroebe/gui/{shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb → universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb} +297 -107
  182. data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb +643 -0
  183. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/format_converter/format_converter.rb +236 -164
  184. data/lib/bioroebe/gui/universal_widgets/gene/gene.rb +278 -0
  185. data/lib/bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb +646 -0
  186. data/lib/bioroebe/gui/{shared_code/levensthein_distance/levensthein_distance_module.rb → universal_widgets/levensthein_distance/levensthein_distance.rb} +313 -88
  187. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/nucleotide_analyser/nucleotide_analyser.rb +281 -189
  188. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/parse_pdb_file/parse_pdb_file.rb +265 -149
  189. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/primer_design_widget/primer_design_widget.rb +337 -263
  190. data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb +408 -0
  191. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/random_sequence/random_sequence.rb +245 -187
  192. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.rb +207 -137
  193. data/lib/bioroebe/gui/universal_widgets/shell/shell.rb +288 -0
  194. data/lib/bioroebe/gui/{gtk3/show_codon_table/misc.rb → universal_widgets/show_codon_table/show_codon_table.rb} +290 -110
  195. data/lib/bioroebe/gui/{shared_code/show_codon_usage/show_codon_usage_module.rb → universal_widgets/show_codon_usage/show_codon_usage.rb} +228 -47
  196. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/sizeseq/sizeseq.rb +151 -69
  197. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/three_to_one/three_to_one.rb +190 -127
  198. data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.rb +211 -152
  199. data/lib/bioroebe/images/images.html +953 -1170
  200. data/lib/bioroebe/images/misc/README.md +6 -0
  201. data/lib/bioroebe/images/misc/activation.avif +0 -0
  202. data/lib/bioroebe/images/misc/inhibition.avif +0 -0
  203. data/lib/bioroebe/images/misc/small_virus_logo.avif +0 -0
  204. data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb} +79 -59
  205. data/lib/bioroebe/matplotlib/matplotlib_generator.rb +1 -1
  206. data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +1 -1
  207. data/lib/bioroebe/misc/ruler.rb +5 -5
  208. data/lib/bioroebe/misc/useful_formulas.rb +3 -3
  209. data/lib/bioroebe/ncbi/efetch.rb +1 -2
  210. data/lib/bioroebe/ngs/phred_quality_score_table.rb +3 -3
  211. data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +3 -6
  212. data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +3 -3
  213. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +6 -10
  214. data/lib/bioroebe/nucleotides/{show_nucleotide_sequence.rb → show_nucleotide_sequence/show_nucleotide_sequence.rb} +377 -255
  215. data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +1 -1
  216. data/lib/bioroebe/palindromes/palindrome_finder.rb +1 -1
  217. data/lib/bioroebe/palindromes/palindrome_generator.rb +2 -10
  218. data/lib/bioroebe/parsers/biolang_parser.rb +1 -1
  219. data/lib/bioroebe/parsers/blosum_parser.rb +14 -19
  220. data/lib/bioroebe/parsers/genbank_parser.rb +2 -6
  221. data/lib/bioroebe/parsers/gff.rb +9 -9
  222. data/lib/bioroebe/parsers/parse_embl.rb +2 -6
  223. data/lib/bioroebe/parsers/stride_parser.rb +4 -12
  224. data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +2 -2
  225. data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +6 -3
  226. data/lib/bioroebe/patterns/profile_pattern.rb +2 -2
  227. data/lib/bioroebe/patterns/rgg_scanner.rb +4 -2
  228. data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb +2 -2
  229. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb +2 -3
  230. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb +4 -4
  231. data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb +2 -2
  232. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb +1 -1
  233. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb +3 -3
  234. data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb +3 -3
  235. data/lib/bioroebe/project/project.rb +3 -1
  236. data/lib/bioroebe/raw_sequence/README.md +8 -8
  237. data/lib/bioroebe/raw_sequence/raw_sequence.rb +11 -2
  238. data/lib/bioroebe/regexes/regexes.rb +1 -2
  239. data/lib/bioroebe/requires/commandline_application.rb +3 -1
  240. data/lib/bioroebe/requires/require_all_pdb_files.rb +1 -1
  241. data/lib/bioroebe/requires/require_all_taxonomy_files.rb +1 -1
  242. data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +10 -0
  243. data/lib/bioroebe/requires/require_colours.rb +1 -1
  244. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +5 -7
  245. data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +1 -1
  246. data/lib/bioroebe/requires/require_the_constants.rb +2 -14
  247. data/lib/bioroebe/requires/require_yaml.rb +7 -5
  248. data/lib/bioroebe/sequence/alignment.rb +1 -1
  249. data/lib/bioroebe/sequence/dna.rb +4 -2
  250. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +22 -8
  251. data/lib/bioroebe/sequence/protein.rb +2 -2
  252. data/lib/bioroebe/sequence/reverse_complement.rb +3 -3
  253. data/lib/bioroebe/sequence/rna.rb +9 -8
  254. data/lib/bioroebe/sequence/sequence.rb +3 -3
  255. data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +0 -0
  256. data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +0 -0
  257. data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +0 -0
  258. data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -1
  259. data/lib/bioroebe/shell/help/class.rb +68 -19
  260. data/lib/bioroebe/shell/menu.rb +5244 -5322
  261. data/lib/bioroebe/shell/{readline/readline.rb → readline.rb} +1 -3
  262. data/lib/bioroebe/shell/shell.rb +11240 -453
  263. data/lib/bioroebe/siRNA/siRNA.rb +3 -3
  264. data/lib/bioroebe/{gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb → sinatra/sinatra_interface.rb} +28 -19
  265. data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb} +731 -754
  266. data/lib/bioroebe/string_matching/find_longest_substring.rb +2 -10
  267. data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +4 -14
  268. data/lib/bioroebe/string_matching/hamming_distance.rb +11 -10
  269. data/lib/bioroebe/string_matching/levensthein.rb +5 -17
  270. data/lib/bioroebe/string_matching/simple_string_comparer.rb +48 -4
  271. data/lib/bioroebe/string_matching/smith_waterman.rb +11 -6
  272. data/lib/bioroebe/svg/glyph.rb +4 -1
  273. data/lib/bioroebe/svg/mini_feature.rb +1 -1
  274. data/lib/bioroebe/svg/page.rb +18 -7
  275. data/lib/bioroebe/svg/svgee.rb +22 -13
  276. data/lib/bioroebe/svg/track.rb +20 -4
  277. data/lib/bioroebe/taxonomy/chart.rb +2 -2
  278. data/lib/bioroebe/taxonomy/class_methods.rb +5 -6
  279. data/lib/bioroebe/taxonomy/constants.rb +1 -1
  280. data/lib/bioroebe/taxonomy/info/info.rb +1 -1
  281. data/lib/bioroebe/taxonomy/info/is_dna.rb +1 -1
  282. data/lib/bioroebe/taxonomy/interactive.rb +1 -2
  283. data/lib/bioroebe/taxonomy/menu.rb +1 -1
  284. data/lib/bioroebe/taxonomy/node.rb +1 -1
  285. data/lib/bioroebe/taxonomy/parse_fasta.rb +4 -2
  286. data/lib/bioroebe/taxonomy/shared.rb +5 -4
  287. data/lib/bioroebe/taxonomy/taxonomy.rb +2 -4
  288. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +3 -45
  289. data/lib/bioroebe/toplevel_methods/{is_on_roebe.rb → roebe.rb} +1 -11
  290. data/lib/bioroebe/toplevel_methods/taxonomy.rb +6 -12
  291. data/lib/bioroebe/toplevel_methods/toplevel_methods.rb +5568 -0
  292. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +4 -3
  293. data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +2 -2
  294. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +16 -9
  295. data/lib/bioroebe/utility_scripts/compacter/compacter.rb +4 -2
  296. data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb +119 -0
  297. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +11 -9
  298. data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb} +13 -4
  299. data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb} +5 -5
  300. data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb} +5 -5
  301. data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb} +16 -15
  302. data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +7 -7
  303. data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +1 -1
  304. data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +2 -0
  305. data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb} +3 -3
  306. data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb} +5 -5
  307. data/lib/bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb +269 -0
  308. data/lib/bioroebe/utility_scripts/find_gene.rb +4 -2
  309. data/lib/bioroebe/utility_scripts/{mirror_repeat.rb → mirror_repeat/mirror_repeat.rb} +5 -5
  310. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +3 -3
  311. data/lib/bioroebe/utility_scripts/{parse_taxonomy.rb → parse_taxonomy/parse_taxonomy.rb} +15 -6
  312. data/lib/bioroebe/utility_scripts/{pathways.rb → pathways/pathways.rb} +4 -3
  313. data/lib/bioroebe/utility_scripts/{permutations.rb → permutations/permutations.rb} +3 -3
  314. data/lib/bioroebe/utility_scripts/punnet/punnet.rb +4 -2
  315. data/lib/bioroebe/utility_scripts/{show_this_dna_sequence.rb → show_this_dna_sequence/show_this_dna_sequence.rb} +1 -1
  316. data/lib/bioroebe/utility_scripts/showorf/showorf.rb +406 -10
  317. data/lib/bioroebe/version/version.rb +2 -2
  318. data/lib/bioroebe/viennarna/rnafold_wrapper.rb +5 -13
  319. data/lib/bioroebe/virus/individual_viruses/README.md +15 -0
  320. data/lib/bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb +40 -0
  321. data/lib/bioroebe/virus/virus.rb +76 -0
  322. data/lib/bioroebe/www/bioroebe.cgi +4 -3
  323. data/lib/bioroebe/www/embeddable_interface.rb +85 -49
  324. data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +6 -6
  325. data/lib/bioroebe/yaml/antisense/antisense.yml +2 -0
  326. data/lib/bioroebe/yaml/blosum/blosum50.yml +6 -0
  327. data/lib/bioroebe/yaml/blosum/blosum90.yml +2 -1
  328. data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +2 -2
  329. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  330. data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
  331. data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +7 -6
  332. data/lib/bioroebe/yaml/humans/human_chromosomes.yml +3 -3
  333. data/lib/bioroebe/yaml/mRNA/mRNA.yml +1 -5
  334. data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +1 -0
  335. data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +2 -1
  336. data/lib/bioroebe/yaml/promoters/35S.yml +3 -1
  337. data/lib/bioroebe/yaml/proteases/proteases.yml +3 -1
  338. data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -1
  339. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +7 -7
  340. data/spec/testing_toplevel_method_editor.rb +1 -1
  341. data/spec/testing_toplevel_method_verbose.rb +1 -1
  342. data/test/testing_dna_to_rna_conversion.rb +1 -1
  343. metadata +127 -235
  344. data/doc/blosum.md +0 -5
  345. data/lib/bioroebe/base/commandline_application/aminoacids.rb +0 -33
  346. data/lib/bioroebe/base/commandline_application/directory.rb +0 -33
  347. data/lib/bioroebe/base/commandline_application/extract.rb +0 -22
  348. data/lib/bioroebe/base/commandline_application/misc.rb +0 -502
  349. data/lib/bioroebe/base/commandline_application/opn.rb +0 -47
  350. data/lib/bioroebe/base/commandline_application/reset.rb +0 -42
  351. data/lib/bioroebe/base/commandline_application/warnings.rb +0 -36
  352. data/lib/bioroebe/base/commandline_application/write_what_into.rb +0 -29
  353. data/lib/bioroebe/base/initialize.rb +0 -18
  354. data/lib/bioroebe/base/misc.rb +0 -129
  355. data/lib/bioroebe/base/namespace.rb +0 -16
  356. data/lib/bioroebe/base/prototype/e_and_ee.rb +0 -24
  357. data/lib/bioroebe/base/prototype/misc.rb +0 -114
  358. data/lib/bioroebe/base/prototype/mkdir.rb +0 -20
  359. data/lib/bioroebe/base/prototype/reset.rb +0 -36
  360. data/lib/bioroebe/colours/misc_colours.rb +0 -80
  361. data/lib/bioroebe/colours/rev.rb +0 -44
  362. data/lib/bioroebe/colours/sdir.rb +0 -21
  363. data/lib/bioroebe/colours/sfancy.rb +0 -21
  364. data/lib/bioroebe/colours/sfile.rb +0 -21
  365. data/lib/bioroebe/colours/simp.rb +0 -21
  366. data/lib/bioroebe/colours/swarn.rb +0 -29
  367. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +0 -147
  368. data/lib/bioroebe/constants/carriage_return.rb +0 -14
  369. data/lib/bioroebe/constants/codon_tables.rb +0 -77
  370. data/lib/bioroebe/constants/database_constants.rb +0 -107
  371. data/lib/bioroebe/constants/files_and_directories.rb +0 -606
  372. data/lib/bioroebe/constants/misc.rb +0 -209
  373. data/lib/bioroebe/constants/newline.rb +0 -14
  374. data/lib/bioroebe/constants/nucleotides.rb +0 -121
  375. data/lib/bioroebe/constants/regex.rb +0 -28
  376. data/lib/bioroebe/constants/roebe.rb +0 -38
  377. data/lib/bioroebe/constants/row_terminator.rb +0 -16
  378. data/lib/bioroebe/constants/tabulator.rb +0 -14
  379. data/lib/bioroebe/constants/unicode.rb +0 -12
  380. data/lib/bioroebe/constants/urls.rb +0 -50
  381. data/lib/bioroebe/gui/gtk +0 -1
  382. data/lib/bioroebe/gui/gtk3/README.md +0 -2
  383. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +0 -306
  384. data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +0 -29
  385. data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -195
  386. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -105
  387. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -188
  388. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +0 -322
  389. data/lib/bioroebe/gui/gtk3/gene/gene.rb +0 -181
  390. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +0 -383
  391. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +0 -174
  392. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +0 -181
  393. data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +0 -101
  394. data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +0 -145
  395. data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +0 -23
  396. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +0 -165
  397. data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +0 -166
  398. data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -82
  399. data/lib/bioroebe/gui/libui/README.md +0 -4
  400. data/lib/bioroebe/gui/libui/alignment/alignment.rb +0 -116
  401. data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -112
  402. data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -60
  403. data/lib/bioroebe/gui/libui/controller/controller.rb +0 -116
  404. data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +0 -161
  405. data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -76
  406. data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +0 -135
  407. data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +0 -118
  408. data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +0 -115
  409. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +0 -190
  410. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +0 -134
  411. data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +0 -89
  412. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +0 -113
  413. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +0 -102
  414. data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +0 -94
  415. data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +0 -216
  416. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +0 -192
  417. data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +0 -72
  418. data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +0 -206
  419. data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -140
  420. data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +0 -262
  421. data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +0 -243
  422. data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +0 -199
  423. data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +0 -519
  424. data/lib/bioroebe/shell/colours/colours.rb +0 -235
  425. data/lib/bioroebe/shell/help/help.rb +0 -25
  426. data/lib/bioroebe/shell/misc.rb +0 -10227
  427. data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +0 -56
  428. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +0 -722
  429. data/lib/bioroebe/toplevel_methods/atomic_composition.rb +0 -198
  430. data/lib/bioroebe/toplevel_methods/base_composition.rb +0 -121
  431. data/lib/bioroebe/toplevel_methods/blast.rb +0 -153
  432. data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +0 -57
  433. data/lib/bioroebe/toplevel_methods/cat.rb +0 -71
  434. data/lib/bioroebe/toplevel_methods/chunked_display.rb +0 -92
  435. data/lib/bioroebe/toplevel_methods/cliner.rb +0 -81
  436. data/lib/bioroebe/toplevel_methods/complement.rb +0 -58
  437. data/lib/bioroebe/toplevel_methods/convert_global_env.rb +0 -39
  438. data/lib/bioroebe/toplevel_methods/databases.rb +0 -73
  439. data/lib/bioroebe/toplevel_methods/delimiter.rb +0 -19
  440. data/lib/bioroebe/toplevel_methods/digest.rb +0 -81
  441. data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +0 -146
  442. data/lib/bioroebe/toplevel_methods/e.rb +0 -20
  443. data/lib/bioroebe/toplevel_methods/editor.rb +0 -21
  444. data/lib/bioroebe/toplevel_methods/esystem.rb +0 -22
  445. data/lib/bioroebe/toplevel_methods/exponential_growth.rb +0 -74
  446. data/lib/bioroebe/toplevel_methods/extract.rb +0 -56
  447. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +0 -269
  448. data/lib/bioroebe/toplevel_methods/frequencies.rb +0 -99
  449. data/lib/bioroebe/toplevel_methods/hamming_distance.rb +0 -60
  450. data/lib/bioroebe/toplevel_methods/infer.rb +0 -66
  451. data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +0 -101
  452. data/lib/bioroebe/toplevel_methods/levensthein.rb +0 -63
  453. data/lib/bioroebe/toplevel_methods/log_directory.rb +0 -109
  454. data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +0 -55
  455. data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +0 -88
  456. data/lib/bioroebe/toplevel_methods/matches.rb +0 -259
  457. data/lib/bioroebe/toplevel_methods/misc.rb +0 -596
  458. data/lib/bioroebe/toplevel_methods/nucleotides.rb +0 -787
  459. data/lib/bioroebe/toplevel_methods/number_of_clones.rb +0 -63
  460. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +0 -79
  461. data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +0 -236
  462. data/lib/bioroebe/toplevel_methods/opn.rb +0 -34
  463. data/lib/bioroebe/toplevel_methods/palindromes.rb +0 -155
  464. data/lib/bioroebe/toplevel_methods/parse.rb +0 -59
  465. data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +0 -68
  466. data/lib/bioroebe/toplevel_methods/rds.rb +0 -24
  467. data/lib/bioroebe/toplevel_methods/remove.rb +0 -86
  468. data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +0 -35
  469. data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +0 -68
  470. data/lib/bioroebe/toplevel_methods/rna_splicing.rb +0 -73
  471. data/lib/bioroebe/toplevel_methods/rnalfold.rb +0 -69
  472. data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +0 -116
  473. data/lib/bioroebe/toplevel_methods/shuffleseq.rb +0 -37
  474. data/lib/bioroebe/toplevel_methods/statistics.rb +0 -53
  475. data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +0 -62
  476. data/lib/bioroebe/toplevel_methods/three_delimiter.rb +0 -34
  477. data/lib/bioroebe/toplevel_methods/time_and_date.rb +0 -53
  478. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +0 -31
  479. data/lib/bioroebe/toplevel_methods/truncate.rb +0 -48
  480. data/lib/bioroebe/toplevel_methods/url.rb +0 -36
  481. data/lib/bioroebe/toplevel_methods/verbose.rb +0 -59
  482. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -31
  483. data/lib/bioroebe/utility_scripts/showorf/help.rb +0 -33
  484. data/lib/bioroebe/utility_scripts/showorf/initialize.rb +0 -52
  485. data/lib/bioroebe/utility_scripts/showorf/menu.rb +0 -68
  486. data/lib/bioroebe/utility_scripts/showorf/reset.rb +0 -36
  487. data/lib/bioroebe/utility_scripts/showorf/run.rb +0 -152
  488. data/lib/bioroebe/utility_scripts/showorf/show.rb +0 -97
  489. /data/doc/{german_names_for_the_aminoacids.md → german_names_for_the_aminoacids/german_names_for_the_aminoacids.md} +0 -0
  490. /data/doc/{pdb_ATOM_entry.md → pdb_ATOM_entry/pdb_ATOM_entry.md} +0 -0
  491. /data/doc/{resources.md → resources/resources.md} +0 -0
  492. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/customized_dialog.rb +0 -0
  493. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/anti_sense_strand/anti_sense_strand.config +0 -0
  494. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +0 -0
  495. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +0 -0
  496. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/hamming_distance/hamming_distance.config +0 -0
  497. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/levensthein_distance/levensthein_distance.config +0 -0
  498. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/protein_to_DNA/protein_to_DNA.config +0 -0
  499. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.config +0 -0
  500. /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.config +0 -0
  501. /data/lib/bioroebe/yaml/{base_composition_of_dna.yml → base_composition_of_dna/base_composition_of_dna.yml} +0 -0
  502. /data/lib/bioroebe/yaml/{nuclear_localization_sequences.yml → nuclear_localization_sequences/nuclear_localization_sequences.yml} +0 -0
  503. /data/lib/bioroebe/yaml/{talens.yml → talens/talens.yml} +0 -0
@@ -2,53 +2,78 @@
2
2
  # Encoding: UTF-8
3
3
  # frozen_string_literal: true
4
4
  # =========================================================================== #
5
- # === Bioroebe::GUI::Gtk::RandomSequence
5
+ # === Bioroebe::GUI::UniversalWidgets::RandomSequence
6
6
  #
7
7
  # This small widget can be used to "generate" random aminoacids, or
8
8
  # random DNA sequence or random RNA sequences quickly.
9
+ #
10
+ # Usage example:
11
+ #
12
+ # Bioroebe::GUI::UniversalWidgets::RandomSequence.new(ARGV)
13
+ #
9
14
  # =========================================================================== #
10
- # require 'bioroebe/gui/gtk3/random_sequence/random_sequence.rb'
11
- # Bioroebe::GUI::Gtk::RandomSequence.run
15
+ # require 'bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb'
12
16
  # =========================================================================== #
13
- require 'gtk_paradise/require_gtk3'
17
+ require 'universal_widgets/base/base.rb'
14
18
 
15
19
  module Bioroebe
16
20
 
17
21
  module GUI
18
22
 
19
- module Gtk
23
+ module UniversalWidgets
20
24
 
21
- class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
22
-
23
- require 'bioroebe/aminoacids/create_random_aminoacids.rb'
24
- require 'bioroebe/toplevel_methods/misc.rb'
25
+ class RandomSequence < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::RandomSequence
25
26
 
26
- require 'gtk_paradise/requires/require_the_base_module.rb'
27
- include ::Gtk::BaseModule
27
+ require 'bioroebe/base/commandline_application/commandline_arguments.rb'
28
+ include ::Bioroebe::CommandlineArguments
28
29
 
29
30
  require 'bioroebe/constants/GUIs.rb'
30
- include ::Bioroebe::GUI::Gtk
31
31
  include Bioroebe::GUI
32
32
 
33
- # ========================================================================= #
34
- # === NAMESPACE
35
- # ========================================================================= #
36
- NAMESPACE = inspect
33
+ require 'bioroebe/toplevel_methods/toplevel_methods.rb'
34
+ require 'bioroebe/aminoacids/create_random_aminoacids.rb'
37
35
 
38
36
  # ========================================================================= #
39
37
  # === TITLE
38
+ #
39
+ # Specify which title to use for this widget.
40
40
  # ========================================================================= #
41
41
  TITLE = 'Random Sequence - for DNA, RNA and aminoacids'
42
42
 
43
43
  # ========================================================================= #
44
44
  # === WIDTH
45
45
  # ========================================================================= #
46
- WIDTH = '45% or minimum 1200px'
46
+ WIDTH = '75% or 1200px minimum'
47
47
 
48
48
  # ========================================================================= #
49
49
  # === HEIGHT
50
50
  # ========================================================================= #
51
- HEIGHT = '45% or minimum 980px'
51
+ HEIGHT = '55% or 980px minimum'
52
+
53
+ # ========================================================================= #
54
+ # === FONT_LARGE
55
+ # ========================================================================= #
56
+ FONT_LARGE = 'Calibri 32'
57
+
58
+ # ========================================================================= #
59
+ # === MONOSPACED_FONT
60
+ #
61
+ # When this font is changed, don't forget to also change the font
62
+ # at SMALLER_FONT.
63
+ # ========================================================================= #
64
+ MONOSPACED_FONT = :hack_22
65
+ USE_THIS_FONT = MONOSPACED_FONT
66
+ USE_THIS_MONOFONT = MONOSPACED_FONT
67
+
68
+ # ========================================================================= #
69
+ # === SMALLER_FONT
70
+ # ========================================================================= #
71
+ SMALLER_FONT = :hack_16
72
+
73
+ # ========================================================================= #
74
+ # === USE_THIS_SLIGHTLY_SMALLER_FONT
75
+ # ========================================================================= #
76
+ USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
52
77
 
53
78
  # ========================================================================= #
54
79
  # === USE_THIS_HEADER
@@ -60,20 +85,14 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
60
85
  # ========================================================================= #
61
86
  GENERATE_N_AMINOACIDS_BY_DEFAULT = 15
62
87
 
63
- # ========================================================================= #
64
- # === USE_THIS_FONT
65
- # ========================================================================= #
66
- USE_THIS_FONT = :dejavu_condensed_22
67
-
68
88
  # ========================================================================= #
69
89
  # === initialize
70
90
  # ========================================================================= #
71
91
  def initialize(
72
- commandline_arguments = ARGV,
92
+ commandline_arguments = nil,
73
93
  run_already = true
74
94
  )
75
- super(:vertical)
76
- register_sigint
95
+ determine_the_GUI_to_be_used(commandline_arguments)
77
96
  reset
78
97
  set_commandline_arguments(
79
98
  commandline_arguments
@@ -85,18 +104,23 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
85
104
  # === reset (reset tag)
86
105
  # ========================================================================= #
87
106
  def reset
107
+ super() if respond_to?(:super)
88
108
  reset_the_internal_variables
109
+ reset_the_base_module # This must come after reset_the_internal_variables().
110
+ infer_the_namespace
89
111
  # ======================================================================= #
90
112
  # === @configuration
91
113
  # ======================================================================= #
92
- @configuration = [true, __dir__, NAMESPACE]
114
+ @configuration = [true, __dir__, namespace?]
115
+ # ======================================================================= #
116
+ # === Set the title, width, height and the font in use.
117
+ # ======================================================================= #
93
118
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
119
+ handle_CSS if use_gtk3?
94
120
  # ======================================================================= #
95
121
  # === @list_store
96
122
  # ======================================================================= #
97
123
  @list_store = nil
98
- handle_CSS
99
- infer_the_size_automatically
100
124
  end
101
125
 
102
126
  # ========================================================================= #
@@ -114,76 +138,129 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
114
138
  end
115
139
 
116
140
  # ========================================================================= #
117
- # === aminoacid_sequence?
141
+ # === main_font?
118
142
  # ========================================================================= #
119
- def aminoacid_sequence?
120
- @entry_containing_the_sequence.text?.to_s
121
- end; alias sequence? aminoacid_sequence? # === sequence?
122
- alias main_sequence? aminoacid_sequence? # === main_sequence?
143
+ def main_font?
144
+ USE_THIS_FONT
145
+ end
123
146
 
124
147
  # ========================================================================= #
125
- # === do_open_a_file_and_then_set_the_correct_values
148
+ # === slightly_smaller_font?
126
149
  # ========================================================================= #
127
- def do_open_a_file_and_then_set_the_correct_values
128
- filename = ::Gtk.select_file(self) {{ # @parent_widget should be of Gtk::Window class or subclass.
129
- show_hidden: true,
130
- add_these_shortcut_folders: ::Bioroebe.log_dir?,
131
- current_folder: ::Bioroebe.log_dir?
132
- }}
133
- if File.exist? filename
134
- _ = filename
135
- if _.end_with? '.fasta'
136
- require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
137
- sequence = Bioroebe.parse_fasta_file(_).sequence?
138
- set_main_input(sequence)
139
- do_evaluate_the_sequence
140
- else
141
- set_main_input(File.read(_).strip)
142
- end
143
- end
150
+ def slightly_smaller_font?
151
+ USE_THIS_SLIGHTLY_SMALLER_FONT
144
152
  end
145
153
 
146
154
  # ========================================================================= #
147
- # === enable_proper_sorting_for_the_list_store
155
+ # === handle_CSS_rules (CSS tag, css tag)
148
156
  # ========================================================================= #
149
- def enable_proper_sorting_for_the_list_store
157
+ def handle_CSS_rules
158
+ use_gtk_paradise_project_css_file
159
+ append_project_css_file
160
+ add_these_custom_CSS_rules '
161
+ '
162
+ apply_the_CSS_rules
163
+ end; alias handle_CSS handle_CSS_rules # === handle_CSS
164
+
165
+ # ========================================================================= #
166
+ # === create_the_copy_to_clipboard_button
167
+ # ========================================================================= #
168
+ def create_the_copy_to_clipboard_button
150
169
  # ======================================================================= #
151
- # Sort the number-of-entries found entry a bit differently. This
152
- # will sort by putting the most frequently occurring aminoacids
153
- # or DNA/RNA nucleotides on top.
170
+ # === @button_copy_to_clipboard
154
171
  # ======================================================================= #
155
- @list_store.set_sort_func(1) { |_model, iter1, iter2|
156
- iter2[1].to_i <=> iter1[1].to_i
172
+ @button_copy_to_clipboard = bold_button('_Copy to the xorg-clipboard',
173
+ self, :use_mnemonic) {
174
+ :do_copy_to_the_clipboard
157
175
  }
176
+ @button_copy_to_clipboard.hint = 'This will <b>copy the aminoacid '\
177
+ 'sequence</b> to the <b>xorg-clipboard</b>.'
178
+ @button_copy_to_clipboard.set_name('button1')
158
179
  end
159
180
 
160
181
  # ========================================================================= #
161
- # === on_right_click_in_the_tree_view_deselect_the_selection
182
+ # === do_generate_a_random_sequence
183
+ #
184
+ # This is the method that will be run whenever a new random aminoacid
185
+ # sequence is to be generated.
162
186
  # ========================================================================= #
163
- def on_right_click_in_the_tree_view_deselect_the_selection
164
- @tree_view.on_right_mouse_button_clicked {|widget, event|
165
- @tree_view.deselect_everything
166
- }
187
+ def do_generate_a_random_sequence(
188
+ n_aminoacids = :default
189
+ )
190
+ case n_aminoacids
191
+ when nil, :default
192
+ n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
193
+ end
194
+ n_aminoacids = n_aminoacids.to_s
195
+ # ======================================================================= #
196
+ # We also must update the entry that displays the aminoacids. We have
197
+ # to check whether we use aminoacids or not, though.
198
+ # ======================================================================= #
199
+ case mode?
200
+ when /RNA/i,
201
+ /DNA/i
202
+ use_this_as_the_new_sequence = :: Bioroebe.generate_random_dna_sequence(n_aminoacids).to_s
203
+ array1 = Bioroebe::DNA_NUCLEOTIDES
204
+ if mode?.to_s == 'RNA'
205
+ use_this_as_the_new_sequence = ::Bioroebe.generate_random_rna_sequence(n_aminoacids).to_s
206
+ array1 = Bioroebe::RNA_NUCLEOTIDES
207
+ end
208
+ hash = {}
209
+ array1.each {|this_key|
210
+ hash[this_key] = 0
211
+ }
212
+ use_this_as_the_new_sequence.chars.each {|this_nucleotide|
213
+ hash[this_nucleotide.to_s] += 1
214
+ }
215
+ array2 = hash.values.map {|entry| entry.to_s }
216
+ else # else assume protein sequence
217
+ use_this_as_the_new_sequence = ::Bioroebe.create_random_aminoacids(n_aminoacids).to_s
218
+ array1 = ::Bioroebe.return_array_of_common_aminoacids
219
+ array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_as_the_new_sequence).values.map(&:to_s)
220
+ end
221
+ @entry_containing_the_sequence.set_content(use_this_as_the_new_sequence)
222
+ # ======================================================================= #
223
+ # Next we have to build up our array, which is then passed into the
224
+ # list-store.
225
+ # ======================================================================= #
226
+ array = array1.zip(array2) # Zip it up with 0-values here.
227
+ # ======================================================================= #
228
+ # Next, populate the liststore with the new data - since as of July
229
+ # 2022 we will sort it based on most aminoacids though:
230
+ # ======================================================================= #
231
+ array = array.sort_by {|a, b| b }.reverse # This sorts by highest first.
232
+ ::Gtk.populate_this_liststore(@list_store, array)
233
+ end
234
+
235
+ # ========================================================================= #
236
+ # === create_the_skeleton (create tag, skeleton tag)
237
+ # ========================================================================= #
238
+ def create_the_skeleton
239
+ create_the_buttons # Call this before the top_bar is created.
240
+ create_statistical_information # Call this before the top-bar is created.
241
+ create_the_top_bar
242
+ create_the_entries
167
243
  end
168
244
 
169
245
  # ========================================================================= #
170
- # === create_the_buttons (buttons tag)
246
+ # === create_the_buttons (buttons tag)
171
247
  # ========================================================================= #
172
248
  def create_the_buttons
173
249
  # ======================================================================= #
174
250
  # === @clear_button
175
251
  # ======================================================================= #
176
- @clear_button = bold_button('_Clear the table above')
177
- @clear_button.hint = 'Clear the above dataset / table'
178
- @clear_button.on_clicked {
179
- do_clear_the_list_store
252
+ @clear_button = bold_button('_Clear the table above', self, :use_mnemonics) {
253
+ :do_clear_the_list_store
180
254
  }
255
+ @clear_button.hint = 'Clear the above dataset / table'
181
256
  @clear_button.set_name('button1')
182
257
  # ======================================================================= #
183
258
  # === @button_for_generating_a_new_random_sequence
184
259
  # ======================================================================= #
185
260
  @button_for_generating_a_new_random_sequence = bold_button(
186
- '_Generate a random aminoacid sequence'
261
+ '_Generate a random aminoacid sequence',
262
+ self,
263
+ :use_mnemonics
187
264
  ) {{ # Add a tooltip.
188
265
  tooltip: 'Clicking on this button will <b>generate a random '\
189
266
  'aminoacid sequence</b>. Do not set a too high value '\
@@ -239,18 +316,17 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
239
316
  # ========================================================================= #
240
317
  def create_the_top_bar
241
318
  @top_bar = gtk_top_bar
242
- button_open_file = gtk_button('_Open File')
319
+ button_open_file = button('_Open File', self, :use_mnemonics) {
320
+ :do_open_a_file_and_then_set_the_correct_values
321
+ }
243
322
  button_open_file.hint = 'Click on this button to open a local FASTA '\
244
323
  'file.'
245
- button_open_file.on_clicked {
246
- do_open_a_file_and_then_set_the_correct_values
247
- }
248
324
  button_open_file.bblack1
249
325
  @top_bar.add(button_open_file)
250
326
  # ======================================================================= #
251
327
  # === @combo_box_for_the_sequence_type
252
328
  # ======================================================================= #
253
- @combo_box_for_the_sequence_type = gtk_combo_box_entry(
329
+ @combo_box_for_the_sequence_type = combo_box_entry(
254
330
  %w( aminoacid DNA RNA )
255
331
  )
256
332
  @combo_box_for_the_sequence_type.first_is_active
@@ -332,24 +408,6 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
332
408
  ::Gtk.populate_this_liststore(@list_store, array)
333
409
  end
334
410
 
335
- # ========================================================================= #
336
- # === connect_skeleton (connect tag)
337
- # ========================================================================= #
338
- def connect_skeleton
339
- abort_on_exception
340
- minimal(@top_bar, 3)
341
- minimal(@entry_containing_the_sequence, 3)
342
- minimal(@button_for_generating_a_new_random_sequence, 3)
343
- minimal(@entry_for_n_entries_in_the_sequence, 3)
344
- hbox_for_the_button_copy_to_clipboard = gtk_hbox
345
- hbox_for_the_button_copy_to_clipboard.minimal(@button_copy_to_clipboard)
346
- hbox_for_the_button_copy_to_clipboard.align_into_the_center
347
- minimal(hbox_for_the_button_copy_to_clipboard, 3)
348
- minimal(@statistical_widget_top_panel, 0)
349
- maximal(@statistical_widget, 3)
350
- show_all
351
- end
352
-
353
411
  # ========================================================================= #
354
412
  # === do_copy_to_the_clipboard
355
413
  # ========================================================================= #
@@ -378,7 +436,7 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
378
436
  # ======================================================================= #
379
437
  # === @entry_containing_the_sequence
380
438
  # ======================================================================= #
381
- @entry_containing_the_sequence = gtk_entry
439
+ @entry_containing_the_sequence = create_entry
382
440
  @entry_containing_the_sequence.on_click_select_everything
383
441
  @entry_containing_the_sequence.yellow_background
384
442
  @entry_containing_the_sequence.bblack1
@@ -386,7 +444,7 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
386
444
  # Add the entry that allows the user to control how many aminoacids
387
445
  # will be "generated".
388
446
  # ======================================================================= #
389
- @entry_for_n_entries_in_the_sequence = gtk_entry { :align_center }
447
+ @entry_for_n_entries_in_the_sequence = create_entry { :align_center }
390
448
  @entry_for_n_entries_in_the_sequence.set_text(GENERATE_N_AMINOACIDS_BY_DEFAULT.to_s)
391
449
  @entry_for_n_entries_in_the_sequence.yellow_background
392
450
  @entry_for_n_entries_in_the_sequence.on_click_select_everything
@@ -406,7 +464,7 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
406
464
  # ========================================================================= #
407
465
  def create_statistical_information
408
466
  create_statistical_top_panel
409
- @statistical_widget = gtk_vbox
467
+ @statistical_widget = create_vbox
410
468
  # ======================================================================= #
411
469
  # Next we must create the widget that can hold the hash. This will
412
470
  # be a list-store that can be dynamically updated.
@@ -420,11 +478,11 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
420
478
  # ======================================================================= #
421
479
  @tree_view, @list_store = tree_widget_with_two_columns_per_row(array)
422
480
  do_properly_setup_the_tree_view
423
- scrolled_window = gtk_scrolled_window(@tree_view)
481
+ scrolled_window = create_scrolled_window(@tree_view)
424
482
  scrolled_window.set_border_width(10)
425
483
  scrolled_window.bblack1
426
484
  @statistical_widget.maximal(scrolled_window, 5)
427
- hbox1 = gtk_hbox
485
+ hbox1 = create_hbox
428
486
  hbox1.minimal(@clear_button)
429
487
  hbox1.align_into_the_center
430
488
  @statistical_widget.minimal(hbox1, 2)
@@ -453,121 +511,121 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
453
511
  end
454
512
 
455
513
  # ========================================================================= #
456
- # === create_the_copy_to_clipboard_button
514
+ # === run (run tag)
457
515
  # ========================================================================= #
458
- def create_the_copy_to_clipboard_button
459
- # ======================================================================= #
460
- # === @button_copy_to_clipboard
461
- # ======================================================================= #
462
- @button_copy_to_clipboard = bold_button('_Copy to the xorg-clipboard')
463
- @button_copy_to_clipboard.hint = 'This will <b>copy the aminoacid '\
464
- 'sequence</b> to the <b>xorg-clipboard</b>.'
465
- @button_copy_to_clipboard.on_clicked {
466
- do_copy_to_the_clipboard
467
- }
468
- @button_copy_to_clipboard.set_name('button1')
516
+ def run
517
+ run_super
469
518
  end
470
519
 
471
520
  # ========================================================================= #
472
- # === create_skeleton (create tag)
521
+ # === aminoacid_sequence?
473
522
  # ========================================================================= #
474
- def create_skeleton
475
- create_the_buttons # Call this before the top_bar is created.
476
- create_statistical_information # Call this before the top-bar is created.
477
- create_the_top_bar
478
- create_the_entries
479
- end
523
+ def aminoacid_sequence?
524
+ @entry_containing_the_sequence.text?.to_s
525
+ end; alias sequence? aminoacid_sequence? # === sequence?
526
+ alias main_sequence? aminoacid_sequence? # === main_sequence?
480
527
 
481
528
  # ========================================================================= #
482
- # === handle_CSS
529
+ # === do_open_a_file_and_then_set_the_correct_values
483
530
  # ========================================================================= #
484
- def handle_CSS
485
- use_gtk_paradise_project_css_file
486
- use_project_css_file
487
- apply_the_CSS
531
+ def do_open_a_file_and_then_set_the_correct_values
532
+ filename = ::Gtk.select_file(self) {{ # @parent_widget should be of Gtk::Window class or subclass.
533
+ show_hidden: true,
534
+ add_these_shortcut_folders: ::Bioroebe.log_dir?,
535
+ current_folder: ::Bioroebe.log_dir?
536
+ }}
537
+ if File.exist? filename
538
+ _ = filename
539
+ if _.end_with? '.fasta'
540
+ require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
541
+ sequence = Bioroebe.parse_fasta_file(_).sequence?
542
+ set_main_input(sequence)
543
+ do_evaluate_the_sequence
544
+ else
545
+ set_main_input(File.read(_).strip)
546
+ end
547
+ end
488
548
  end
489
549
 
490
550
  # ========================================================================= #
491
- # === do_generate_a_random_sequence
492
- #
493
- # This is the method that will be run whenever a new random aminoacid
494
- # sequence is to be generated.
551
+ # === enable_proper_sorting_for_the_list_store
495
552
  # ========================================================================= #
496
- def do_generate_a_random_sequence(
497
- n_aminoacids = :default
498
- )
499
- case n_aminoacids
500
- when nil, :default
501
- n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
502
- end
503
- n_aminoacids = n_aminoacids.to_s
504
- # ======================================================================= #
505
- # We also must update the entry that displays the aminoacids. We have
506
- # to check whether we use aminoacids or not, though.
507
- # ======================================================================= #
508
- case mode?
509
- when /RNA/i,
510
- /DNA/i
511
- use_this_as_the_new_sequence = :: Bioroebe.generate_random_dna_sequence(n_aminoacids).to_s
512
- array1 = Bioroebe::DNA_NUCLEOTIDES
513
- if mode?.to_s == 'RNA'
514
- use_this_as_the_new_sequence = ::Bioroebe.generate_random_rna_sequence(n_aminoacids).to_s
515
- array1 = Bioroebe::RNA_NUCLEOTIDES
516
- end
517
- hash = {}
518
- array1.each {|this_key|
519
- hash[this_key] = 0
520
- }
521
- use_this_as_the_new_sequence.chars.each {|this_nucleotide|
522
- hash[this_nucleotide.to_s] += 1
523
- }
524
- array2 = hash.values.map {|entry| entry.to_s }
525
- else # else assume protein sequence
526
- use_this_as_the_new_sequence = ::Bioroebe.create_random_aminoacids(n_aminoacids).to_s
527
- array1 = ::Bioroebe.return_array_of_common_aminoacids
528
- array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_as_the_new_sequence).values.map(&:to_s)
529
- end
530
- @entry_containing_the_sequence.set_content(use_this_as_the_new_sequence)
531
- # ======================================================================= #
532
- # Next we have to build up our array, which is then passed into the
533
- # list-store.
534
- # ======================================================================= #
535
- array = array1.zip(array2) # Zip it up with 0-values here.
553
+ def enable_proper_sorting_for_the_list_store
536
554
  # ======================================================================= #
537
- # Next, populate the liststore with the new data - since as of July
538
- # 2022 we will sort it based on most aminoacids though:
555
+ # Sort the number-of-entries found entry a bit differently. This
556
+ # will sort by putting the most frequently occurring aminoacids
557
+ # or DNA/RNA nucleotides on top.
539
558
  # ======================================================================= #
540
- array = array.sort_by {|a, b| b }.reverse # This sorts by highest first.
541
- ::Gtk.populate_this_liststore(@list_store, array)
559
+ @list_store.set_sort_func(1) { |_model, iter1, iter2|
560
+ iter2[1].to_i <=> iter1[1].to_i
561
+ }
542
562
  end
543
563
 
544
564
  # ========================================================================= #
545
- # === run
565
+ # === on_right_click_in_the_tree_view_deselect_the_selection
546
566
  # ========================================================================= #
547
- def run
548
- super()
567
+ def on_right_click_in_the_tree_view_deselect_the_selection
568
+ @tree_view.on_right_mouse_button_clicked {|widget, event|
569
+ @tree_view.deselect_everything
570
+ }
571
+ end
572
+
573
+ # ========================================================================= #
574
+ # === connect_the_skeleton (connect tag, skeleton tag)
575
+ # ========================================================================= #
576
+ def connect_the_skeleton
577
+ abort_on_exception
578
+
579
+ vbox1 = create_vbox
580
+ vbox1.minimal(@top_bar, 3)
581
+ vbox1.minimal(@entry_containing_the_sequence, 3)
582
+ vbox1.minimal(@button_for_generating_a_new_random_sequence, 3)
583
+ vbox1.minimal(@entry_for_n_entries_in_the_sequence, 3)
584
+ hbox_for_the_button_copy_to_clipboard = create_hbox
585
+ hbox_for_the_button_copy_to_clipboard.minimal(@button_copy_to_clipboard)
586
+ hbox_for_the_button_copy_to_clipboard.align_into_the_center
587
+ vbox1.minimal(hbox_for_the_button_copy_to_clipboard, 3)
588
+ vbox1.minimal(@statistical_widget_top_panel, 0)
589
+ vbox1.maximal(@statistical_widget, 3)
590
+
591
+ window = runner_widget(nil, width?, height?, title?)
592
+ window << vbox1
593
+
594
+ ::UniversalWidgets.set_main_window(window)
595
+ upon_delete_event_quit_the_application
596
+ window.use_this_font = font?
597
+ window.show_all
598
+ window.set_size_request(width?, height?)
599
+ window.set_default_size(width?, height?)
600
+ window.set_padding(padding?)
601
+ window.set_border_size(border_size?)
602
+ window.top_left
603
+ run_main
604
+ end
605
+
606
+ # ========================================================================= #
607
+ # === Bioroebe::GUI::UniversalWidgets::RandomSequence[]
608
+ # ========================================================================= #
609
+ def self.[](i = ARGV)
610
+ new(i)
549
611
  end
550
612
 
551
613
  # ========================================================================= #
552
- # === Bioroebe::GUI::Gtk::RandomSequence.start_gui_application
614
+ # === Bioroebe::GUI::Gtk::RandomSequence.run
553
615
  # ========================================================================= #
554
- def self.start_gui_application(
616
+ def self.run(
555
617
  i = ARGV
556
618
  )
557
- require 'gtk_paradise/run'
558
- # ======================================================================= #
559
- # Instantiate a new GUI next.
560
- # ======================================================================= #
561
- _ = ::Bioroebe::GUI::Gtk::RandomSequence.new(i)
562
- r = ::Gtk.run
563
- r << _
564
- r.background_colour :white
565
- r.easy_exit
566
- r.automatic_top_left_then_run
567
- end; self.instance_eval { alias run start_gui_application } # === RandomSequence.run
619
+ r = ::Gtk.runner_factory(
620
+ ::Bioroebe::GUI::Gtk::RandomSequence.new(i)
621
+ )
622
+ r.background_colour(:white)
623
+ return r
624
+ end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::RandomSequence.run_gtk3_widget
625
+ self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::RandomSequence.start_gui_application
568
626
 
569
627
  end; end; end; end
570
628
 
571
629
  if __FILE__ == $PROGRAM_NAME
572
- Bioroebe::GUI::Gtk::RandomSequence.run
630
+ Bioroebe::GUI::UniversalWidgets::RandomSequence.new(ARGV)
573
631
  end # gtkrandomsequence