bioroebe 0.10.80 → 0.12.24

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (301) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3946 -2817
  3. data/bin/bioroebe +13 -2
  4. data/bin/bioroebe_hash +7 -0
  5. data/bin/codon_to_aminoacid +6 -4
  6. data/bin/compacter +7 -0
  7. data/bin/plain_palindrome +7 -0
  8. data/bioroebe.gemspec +3 -3
  9. data/doc/README.gen +3918 -2793
  10. data/doc/quality_control/commandline_applications.md +3 -3
  11. data/doc/statistics/statistics.md +7 -7
  12. data/doc/todo/bioroebe_GUI_todo.md +19 -14
  13. data/doc/todo/bioroebe_java_todo.md +22 -0
  14. data/doc/todo/bioroebe_todo.md +2075 -2620
  15. data/lib/bioroebe/C++/DNA.cpp +69 -0
  16. data/lib/bioroebe/C++/RNA.cpp +58 -0
  17. data/lib/bioroebe/C++/sequence.cpp +35 -0
  18. data/lib/bioroebe/abstract/README.md +1 -0
  19. data/lib/bioroebe/abstract/features.rb +29 -0
  20. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  21. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  22. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  23. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  24. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  25. data/lib/bioroebe/base/base_module/base_module.rb +36 -0
  26. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  27. data/lib/bioroebe/base/commandline_application/commandline_application.rb +13 -9
  28. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +24 -19
  29. data/lib/bioroebe/base/commandline_application/misc.rb +66 -49
  30. data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
  31. data/lib/bioroebe/base/commandline_application/reset.rb +5 -3
  32. data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +42 -0
  33. data/lib/bioroebe/base/misc.rb +35 -0
  34. data/lib/bioroebe/base/prototype/misc.rb +15 -9
  35. data/lib/bioroebe/base/prototype/reset.rb +10 -0
  36. data/lib/bioroebe/cleave_and_digest/digestion.rb +10 -2
  37. data/lib/bioroebe/cleave_and_digest/trypsin.rb +104 -50
  38. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
  39. data/lib/bioroebe/codons/codons.rb +1 -1
  40. data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +208 -59
  41. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
  42. data/lib/bioroebe/codons/show_codon_tables.rb +8 -3
  43. data/lib/bioroebe/codons/show_codon_usage.rb +15 -4
  44. data/lib/bioroebe/colours/rev.rb +4 -1
  45. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  46. data/lib/bioroebe/constants/database_constants.rb +1 -1
  47. data/lib/bioroebe/constants/files_and_directories.rb +31 -4
  48. data/lib/bioroebe/constants/misc.rb +20 -0
  49. data/lib/bioroebe/constants/nucleotides.rb +7 -0
  50. data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +109 -39
  51. data/lib/bioroebe/count/count_amount_of_aminoacids.rb +3 -2
  52. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  53. data/lib/bioroebe/cpp +1 -0
  54. data/lib/bioroebe/crystal/README.md +2 -0
  55. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  56. data/lib/bioroebe/data/README.md +11 -8
  57. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  58. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  59. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_alpha_HBB_mRNA.fasta +9 -0
  60. data/lib/bioroebe/data/fasta/human/Homo_sapiens_hemoglobin_subunit_beta_HBB_mRNA.fasta +8 -0
  61. data/lib/bioroebe/data/fasta/human/README.md +2 -0
  62. data/lib/bioroebe/dotplots/advanced_dotplot.rb +1 -1
  63. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
  64. data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
  65. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
  66. data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
  67. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
  68. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
  69. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  70. data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +10 -3
  71. data/lib/bioroebe/enzymes/restriction_enzyme.rb +23 -1
  72. data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +65 -0
  73. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
  74. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
  75. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
  76. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
  77. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1518 -7
  78. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
  79. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  80. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
  81. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
  82. data/lib/bioroebe/genome/README.md +4 -0
  83. data/lib/bioroebe/genome/genome.rb +130 -0
  84. data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
  85. data/lib/bioroebe/gui/gtk +1 -0
  86. data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +106 -137
  87. data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +27 -61
  88. data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +1 -1
  89. data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +1 -2
  90. data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +1 -2
  91. data/lib/bioroebe/gui/gtk3/controller/controller.rb +46 -29
  92. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +77 -52
  93. data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +1 -2
  94. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +100 -23
  95. data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +1 -2
  96. data/lib/bioroebe/gui/gtk3/gene/gene.rb +1 -2
  97. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +43 -30
  98. data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +1 -2
  99. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +120 -73
  100. data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +1 -2
  101. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +19 -20
  102. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +20 -13
  103. data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb +1 -2
  104. data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +97 -22
  105. data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +3 -73
  106. data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +1 -2
  107. data/lib/bioroebe/gui/gtk3/sizeseq/sizeseq.rb +1 -2
  108. data/lib/bioroebe/gui/gtk3/three_to_one/three_to_one.rb +1 -2
  109. data/lib/bioroebe/gui/gtk3/www_finder/www_finder.rb +1 -2
  110. data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.class +0 -0
  111. data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.java +104 -0
  112. data/lib/bioroebe/gui/javafx/bioroebe.jar +0 -0
  113. data/lib/bioroebe/gui/javafx/bioroebe.mf +1 -0
  114. data/lib/bioroebe/gui/javafx/module-info.class +0 -0
  115. data/lib/bioroebe/gui/javafx/module-info.java +5 -0
  116. data/lib/bioroebe/gui/jruby/alignment/alignment.rb +165 -0
  117. data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +166 -0
  118. data/lib/bioroebe/gui/libui/alignment/alignment.rb +3 -1
  119. data/lib/bioroebe/gui/libui/controller/controller.rb +116 -0
  120. data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +18 -2
  121. data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +2 -0
  122. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
  123. data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +102 -0
  124. data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +94 -0
  125. data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +18 -16
  126. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  127. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
  128. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
  129. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
  130. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
  131. data/lib/bioroebe/images/FORWARD_PRIMER.png +0 -0
  132. data/lib/bioroebe/images/REVERSE_PRIMER.png +0 -0
  133. data/lib/bioroebe/images/images.html +29845 -0
  134. data/lib/bioroebe/java/README.md +5 -0
  135. data/lib/bioroebe/java/bioroebe/AllInOne.java +1 -0
  136. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  137. data/lib/bioroebe/java/bioroebe/Base.java +39 -5
  138. data/lib/bioroebe/java/bioroebe/IsPalindrome.java +23 -5
  139. data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java +0 -0
  140. data/lib/bioroebe/java/bioroebe/Sequence.java +28 -3
  141. data/lib/bioroebe/java/bioroebe/ToCamelcase.class +0 -0
  142. data/lib/bioroebe/java/bioroebe/ToCamelcase.java +16 -4
  143. data/lib/bioroebe/java/bioroebe/ToRNA.java +43 -0
  144. data/lib/bioroebe/java/bioroebe/ToplevelMethods.java +6 -0
  145. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/BisulfiteTreatment.class} +0 -0
  146. data/lib/bioroebe/java/bioroebe/{Codons.class → src/Codons.class} +0 -0
  147. data/lib/bioroebe/java/bioroebe/src/Codons.java +35 -0
  148. data/lib/bioroebe/java/bioroebe/src/Commandline.class +0 -0
  149. data/lib/bioroebe/java/bioroebe/src/Commandline.java +101 -0
  150. data/lib/bioroebe/java/bioroebe/{Esystem.class → src/Esystem.class} +0 -0
  151. data/lib/bioroebe/java/bioroebe/{Esystem.java → src/Esystem.java} +6 -1
  152. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/GenerateRandomDnaSequence.class} +0 -0
  153. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/GenerateRandomDnaSequence.java} +8 -2
  154. data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.class +0 -0
  155. data/lib/bioroebe/java/bioroebe/src/PartnerNucleotide.java +56 -0
  156. data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/RemoveFile.java} +10 -4
  157. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/RemoveNumbers.class} +0 -0
  158. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/RemoveNumbers.java} +1 -0
  159. data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.class +0 -0
  160. data/lib/bioroebe/java/bioroebe/src/toplevel_methods/BaseComposition.java +75 -0
  161. data/lib/bioroebe/misc/ruler.rb +11 -2
  162. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
  163. data/lib/bioroebe/nucleotides/sanitize_nucleotide_sequence.rb +59 -18
  164. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
  165. data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
  166. data/lib/bioroebe/parsers/gff.rb +1 -9
  167. data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
  168. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
  169. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
  170. data/lib/bioroebe/pdb/parse_pdb_file.rb +4 -10
  171. data/lib/bioroebe/project/project.rb +1 -1
  172. data/lib/bioroebe/python/README.md +1 -0
  173. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  174. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  175. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  176. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  177. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  178. data/lib/bioroebe/python/mymodule.py +8 -0
  179. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  180. data/lib/bioroebe/python/shell/shell.py +19 -0
  181. data/lib/bioroebe/python/to_rna.py +14 -0
  182. data/lib/bioroebe/python/toplevel_methods/convert_dna_to_aminoacid_sequence.py +137 -0
  183. data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
  184. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  185. data/lib/bioroebe/python/toplevel_methods/palindromes.py +52 -0
  186. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  187. data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
  188. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
  189. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  190. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
  191. data/lib/bioroebe/requires/require_cleave_and_digest.rb +3 -1
  192. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  193. data/lib/bioroebe/sequence/alignment.rb +14 -4
  194. data/lib/bioroebe/sequence/dna.rb +1 -0
  195. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  196. data/lib/bioroebe/sequence/protein.rb +105 -3
  197. data/lib/bioroebe/sequence/rna.rb +220 -0
  198. data/lib/bioroebe/sequence/sequence.rb +128 -40
  199. data/lib/bioroebe/shell/menu.rb +3815 -3696
  200. data/lib/bioroebe/shell/misc.rb +9019 -3133
  201. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  202. data/lib/bioroebe/shell/shell.rb +1137 -28
  203. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  204. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  205. data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
  206. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  207. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  208. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  209. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  210. data/lib/bioroebe/taxonomy/help/helpline.rb +2 -2
  211. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  212. data/lib/bioroebe/taxonomy/info/info.rb +18 -11
  213. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  214. data/lib/bioroebe/taxonomy/interactive.rb +140 -104
  215. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  216. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  217. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  218. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  219. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  220. data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
  221. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  222. data/lib/bioroebe/toplevel_methods/digest.rb +18 -8
  223. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
  224. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
  225. data/lib/bioroebe/toplevel_methods/frequencies.rb +8 -1
  226. data/lib/bioroebe/toplevel_methods/misc.rb +175 -11
  227. data/lib/bioroebe/toplevel_methods/nucleotides.rb +118 -46
  228. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  229. data/lib/bioroebe/toplevel_methods/palindromes.rb +75 -47
  230. data/lib/bioroebe/toplevel_methods/taxonomy.rb +3 -3
  231. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  232. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  233. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  234. data/lib/bioroebe/utility_scripts/compacter/compacter.rb +251 -0
  235. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  236. data/lib/bioroebe/utility_scripts/consensus_sequence.rb +6 -6
  237. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  238. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  239. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  240. data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +2 -2
  241. data/lib/bioroebe/utility_scripts/permutations.rb +36 -9
  242. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  243. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  244. data/lib/bioroebe/version/version.rb +2 -2
  245. data/lib/bioroebe/www/embeddable_interface.rb +121 -58
  246. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -71
  247. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  248. data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +17 -17
  249. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  250. data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
  251. data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
  252. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  253. data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +5 -0
  254. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +57 -57
  255. data/spec/README.md +6 -0
  256. data/spec/project_wide_specification/classes.md +5 -0
  257. metadata +107 -70
  258. data/doc/setup.rb +0 -1655
  259. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
  260. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
  261. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
  262. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
  263. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
  264. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
  265. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  266. data/lib/bioroebe/java/bioroebe/AllInOne.class +0 -0
  267. data/lib/bioroebe/java/bioroebe/Cat.class +0 -0
  268. data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
  269. data/lib/bioroebe/java/bioroebe/IsPalindrome.class +0 -0
  270. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  271. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
  272. data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class +0 -0
  273. data/lib/bioroebe/java/bioroebe/ToplevelMethods.class +0 -0
  274. data/lib/bioroebe/java/bioroebe.jar +0 -0
  275. data/lib/bioroebe/shell/add.rb +0 -108
  276. data/lib/bioroebe/shell/assign.rb +0 -360
  277. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  278. data/lib/bioroebe/shell/constants.rb +0 -166
  279. data/lib/bioroebe/shell/download.rb +0 -335
  280. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  281. data/lib/bioroebe/shell/enzymes.rb +0 -310
  282. data/lib/bioroebe/shell/fasta.rb +0 -345
  283. data/lib/bioroebe/shell/gtk.rb +0 -76
  284. data/lib/bioroebe/shell/history.rb +0 -132
  285. data/lib/bioroebe/shell/initialize.rb +0 -217
  286. data/lib/bioroebe/shell/loop.rb +0 -74
  287. data/lib/bioroebe/shell/prompt.rb +0 -107
  288. data/lib/bioroebe/shell/random.rb +0 -289
  289. data/lib/bioroebe/shell/reset.rb +0 -335
  290. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  291. data/lib/bioroebe/shell/search.rb +0 -337
  292. data/lib/bioroebe/shell/sequences.rb +0 -200
  293. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  294. data/lib/bioroebe/shell/startup.rb +0 -127
  295. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  296. data/lib/bioroebe/shell/tk.rb +0 -23
  297. data/lib/bioroebe/shell/user_input.rb +0 -88
  298. data/lib/bioroebe/shell/xorg.rb +0 -45
  299. data/lib/bioroebe/utility_scripts/compacter.rb +0 -131
  300. /data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/BisulfiteTreatment.java} +0 -0
  301. /data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/RemoveFile.class} +0 -0
data/doc/quality_control/commandline_applications.md CHANGED
@@ -6,8 +6,8 @@ commandline should adhere to the following aspects:
6
6
 
7
7
  - Every program should ideally be tested with, at the least, the bare
8
8
  minimum that tests its functionality, in particular all options that
9
- are mentioned via --help.
9
+ are (specifically) mentioned via --help.
10
10
 
11
11
  - Every value that is important for the given commandline program
12
- should be user-changeable, so that a user is never required to
13
- modify the source code on his/her own.
12
+ should be user-changeable (toggle-functionality), so that a user
13
+ is never required to modify the source code on his/her own.
data/doc/statistics/statistics.md CHANGED
@@ -28,13 +28,13 @@ https://bestgems.org/gems/bioroebe
28
28
 
29
29
  Size of the bioroebe-gem itself (showing only a few snapshots):
30
30
 
31
- 0.0.79 - July 19, 2015 ( 86 KB)
32
- 0.0.414 - July 17, 2016 ( 308 KB)
33
- 0.1.075 - January 21, 2018 ( 413 KB)
34
- 0.3.0 - January 18, 2018 ( 536 KB)
35
- 0.3.44 - March 17, 2019 ( 578 KB)
36
- 0.3.77 - August 17, 2019 ( 749 KB) # Includes a large .pdb file, though.
37
- 0.8.80 - August 05, 2021 ( 949 KB)
31
+ 0.0.79 - July 19, 2015 ( 86 KB)
32
+ 0.0.414 - July 17, 2016 ( 308 KB)
33
+ 0.1.075 - January 21, 2018 ( 413 KB)
34
+ 0.3.0 - January 18, 2018 ( 536 KB)
35
+ 0.3.44 - March 17, 2019 ( 578 KB)
36
+ 0.3.77 - August 17, 2019 ( 749 KB) # Includes a large .pdb file, though.
37
+ 0.8.80 - August 05, 2021 ( 949 KB)
38
38
  0.9.75 - December 18, 2021 (1009 KB)
39
39
  0.10.22 - December 24, 2021 (1.09 MB)
40
40
 
data/doc/todo/bioroebe_GUI_todo.md CHANGED
@@ -1,15 +1,20 @@
1
- -------------------------------------------------------------------------
2
- (1) Improve the primer-design widget. It should be fully
3
- functional one day. See also this entry here:
4
-
1
+ --------------------------------------------------------------------------------
2
+ (1) → Improve the primer-design widget. It should be fully
3
+ functional one day. See also this entry here:
5
4
  https://www.geneious.com/tutorials/primer-design-prime/
6
-
7
- gtkprimerdesign
8
- --------------------------------------------------------------------------
9
- (2) enable drag and drop support in the bioroebe gui
10
-
11
- The idea is that we can freely move FASTA sequences and .pdb files
12
- into different widgets. When hitting the target the sequence becomes
13
- available and auto-fills the bioroebe-GUI-widget at hand in a clean,
14
- logical way.
15
- --------------------------------------------------------------------------
5
+ gtkprimerdesign
6
+ --------------------------------------------------------------------------------
7
+ (2) → enable drag and drop support in the bioroebe gui
8
+ The idea is that we can freely move FASTA sequences and .pdb files
9
+ into different widgets. When hitting the target the sequence becomes
10
+ available and auto-fills the bioroebe-GUI-widget at hand in a clean,
11
+ logical way.
12
+ --------------------------------------------------------------------------------
13
+ (3) → jruby erweitern für bioroebe
14
+ ^^^ und das beschreiben.
15
+ also zerst mal die ruby-gtk3 sachen durchgehen und
16
+ dann eben jruby zeugs adaptieren ausgehend davon.
17
+ die ruby-gtk3 widgets 1:1 durchgehen und sie in
18
+ jruby rewriten.
19
+ ^^^
20
+ --------------------------------------------------------------------------------
data/doc/todo/bioroebe_java_todo.md ADDED
@@ -0,0 +1,22 @@
1
+ /Depot/j/toaa ATGGCCGAGATTGTGCTGGAGCACGTCAACAAGAAT --frame1
2
+
3
+ The frame-1 sequence is: (12 aminoacids)
4
+
5
+ MAEIVLEHVNKN
6
+
7
+ /Depot/j/toaa ATGGCCGAGATTGTGCTGGAGCACGTCAACAAGAAT --frame2
8
+
9
+ The frame-2 sequence is: (11 aminoacids)
10
+
11
+ WPRLCWSTSTR
12
+
13
+ /Depot/j/toaa ATGGCCGAGATTGTGCTGGAGCACGTCAACAAGAAT --frame3
14
+
15
+ The frame-3 sequence is: (11 aminoacids)
16
+
17
+ GRDCAGARQQE
18
+
19
+
20
+ ^^^^ add this in java AND add it to
21
+ static native binary
22
+