bioroebe 0.10.80 → 0.11.32

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Files changed (210) hide show
  1. checksums.yaml +4 -4
  2. data/README.md +3209 -2618
  3. data/bin/bioroebe +7 -1
  4. data/bioroebe.gemspec +3 -3
  5. data/doc/README.gen +3208 -2617
  6. data/doc/quality_control/commandline_applications.md +3 -3
  7. data/doc/todo/bioroebe_todo.md +2040 -2615
  8. data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -9
  9. data/lib/bioroebe/aminoacids/codon_percentage.rb +1 -9
  10. data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +1 -9
  11. data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -0
  12. data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +1 -6
  13. data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +18 -8
  14. data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +13 -11
  15. data/lib/bioroebe/base/commandline_application/misc.rb +26 -9
  16. data/lib/bioroebe/base/commandline_application/opn.rb +8 -8
  17. data/lib/bioroebe/base/commandline_application/reset.rb +3 -2
  18. data/lib/bioroebe/base/misc.rb +35 -0
  19. data/lib/bioroebe/base/prototype/misc.rb +11 -1
  20. data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -10
  21. data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +1 -9
  22. data/lib/bioroebe/codons/show_codon_tables.rb +6 -2
  23. data/lib/bioroebe/codons/show_codon_usage.rb +2 -1
  24. data/lib/bioroebe/constants/aminoacids_and_proteins.rb +1 -0
  25. data/lib/bioroebe/constants/database_constants.rb +1 -1
  26. data/lib/bioroebe/constants/files_and_directories.rb +31 -4
  27. data/lib/bioroebe/constants/misc.rb +20 -0
  28. data/lib/bioroebe/count/count_amount_of_nucleotides.rb +3 -0
  29. data/lib/bioroebe/crystal/README.md +2 -0
  30. data/lib/bioroebe/crystal/to_rna.cr +19 -0
  31. data/lib/bioroebe/data/README.md +11 -8
  32. data/lib/bioroebe/data/electron_microscopy/pos_example.pos +396 -0
  33. data/lib/bioroebe/data/electron_microscopy/test_particles.star +36 -0
  34. data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +15 -18
  35. data/lib/bioroebe/{fasta_and_fastq/parse_fasta/run.rb → electron_microscopy/electron_microscopy_module.rb} +16 -8
  36. data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +1 -9
  37. data/lib/bioroebe/electron_microscopy/flipy.rb +83 -0
  38. data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +2 -10
  39. data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +1 -9
  40. data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +4 -9
  41. data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +1 -9
  42. data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +7 -9
  43. data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -5
  44. data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +81 -0
  45. data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +1460 -7
  46. data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +11 -2
  47. data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +27 -12
  48. data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -5
  49. data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +0 -5
  50. data/lib/bioroebe/genome/README.md +4 -0
  51. data/lib/bioroebe/genome/genome.rb +67 -0
  52. data/lib/bioroebe/genomes/genome_pattern.rb +3 -9
  53. data/lib/bioroebe/gui/gtk +1 -0
  54. data/lib/bioroebe/gui/gtk3/controller/controller.rb +45 -27
  55. data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +76 -50
  56. data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +99 -21
  57. data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +42 -28
  58. data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +119 -71
  59. data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +18 -18
  60. data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +19 -11
  61. data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +8 -6
  62. data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +14 -14
  63. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class +0 -0
  64. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class +0 -0
  65. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class +0 -0
  66. data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java +141 -0
  67. data/lib/bioroebe/java/README.md +4 -0
  68. data/lib/bioroebe/java/bioroebe/Sequence.java +25 -1
  69. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.class +0 -0
  70. data/lib/bioroebe/java/bioroebe/{Base.java → src/main/java/bioroebe/Base.java} +15 -2
  71. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.class → src/main/java/bioroebe/BisulfiteTreatment.class} +0 -0
  72. data/lib/bioroebe/java/bioroebe/{BisulfiteTreatment.java → src/main/java/bioroebe/BisulfiteTreatment.java} +0 -0
  73. data/lib/bioroebe/java/bioroebe/{Codons.class → src/main/java/bioroebe/Codons.class} +0 -0
  74. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java +34 -0
  75. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.class +0 -0
  76. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java +95 -0
  77. data/lib/bioroebe/java/bioroebe/{Esystem.class → src/main/java/bioroebe/Esystem.class} +0 -0
  78. data/lib/bioroebe/java/bioroebe/{Esystem.java → src/main/java/bioroebe/Esystem.java} +0 -0
  79. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.class → src/main/java/bioroebe/GenerateRandomDnaSequence.class} +0 -0
  80. data/lib/bioroebe/java/bioroebe/{GenerateRandomDnaSequence.java → src/main/java/bioroebe/GenerateRandomDnaSequence.java} +8 -2
  81. data/lib/bioroebe/java/bioroebe/{IsPalindrome.class → src/main/java/bioroebe/IsPalindrome.class} +0 -0
  82. data/lib/bioroebe/java/bioroebe/{IsPalindrome.java → src/main/java/bioroebe/IsPalindrome.java} +5 -1
  83. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.class +0 -0
  84. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java +56 -0
  85. data/lib/bioroebe/java/bioroebe/{RemoveFile.class → src/main/java/bioroebe/RemoveFile.class} +0 -0
  86. data/lib/bioroebe/java/bioroebe/{RemoveFile.java → src/main/java/bioroebe/RemoveFile.java} +10 -4
  87. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.class → src/main/java/bioroebe/RemoveNumbers.class} +0 -0
  88. data/lib/bioroebe/java/bioroebe/{RemoveNumbers.java → src/main/java/bioroebe/RemoveNumbers.java} +1 -0
  89. data/lib/bioroebe/java/bioroebe/{ToCamelcase.class → src/main/java/bioroebe/ToCamelcase.class} +0 -0
  90. data/lib/bioroebe/java/bioroebe/{ToCamelcase.java → src/main/java/bioroebe/ToCamelcase.java} +3 -3
  91. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.class +0 -0
  92. data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java +42 -0
  93. data/lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.class +0 -0
  94. data/lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.java +73 -0
  95. data/lib/bioroebe/misc/ruler.rb +1 -0
  96. data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +1 -9
  97. data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +7 -7
  98. data/lib/bioroebe/parsers/genbank_parser.rb +347 -26
  99. data/lib/bioroebe/parsers/gff.rb +1 -9
  100. data/lib/bioroebe/patterns/scan_for_repeat.rb +1 -5
  101. data/lib/bioroebe/pdb/fetch_fasta_sequence_from_pdb.rb +1 -9
  102. data/lib/bioroebe/pdb/parse_mmCIF_file.rb +1 -9
  103. data/lib/bioroebe/pdb/parse_pdb_file.rb +1 -9
  104. data/lib/bioroebe/project/project.rb +1 -1
  105. data/lib/bioroebe/python/README.md +1 -0
  106. data/lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc +0 -0
  107. data/lib/bioroebe/python/gui/gtk3/all_in_one.css +4 -0
  108. data/lib/bioroebe/python/gui/gtk3/all_in_one.py +59 -0
  109. data/lib/bioroebe/python/gui/gtk3/widget1.py +20 -0
  110. data/lib/bioroebe/python/gui/tkinter/all_in_one.py +91 -0
  111. data/lib/bioroebe/python/mymodule.py +8 -0
  112. data/lib/bioroebe/python/protein_to_dna.py +33 -0
  113. data/lib/bioroebe/python/shell/shell.py +19 -0
  114. data/lib/bioroebe/python/to_rna.py +14 -0
  115. data/lib/bioroebe/python/toplevel_methods/esystem.py +12 -0
  116. data/lib/bioroebe/python/toplevel_methods/open_in_browser.py +20 -0
  117. data/lib/bioroebe/python/toplevel_methods/palindromes.py +42 -0
  118. data/lib/bioroebe/python/toplevel_methods/rds.py +13 -0
  119. data/lib/bioroebe/python/toplevel_methods/shuffleseq.py +23 -0
  120. data/lib/bioroebe/python/toplevel_methods/three_delimiter.py +37 -0
  121. data/lib/bioroebe/python/toplevel_methods/time_and_date.py +43 -0
  122. data/lib/bioroebe/python/toplevel_methods/to_camelcase.py +21 -0
  123. data/lib/bioroebe/requires/require_the_bioroebe_project.rb +3 -1
  124. data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +28 -25
  125. data/lib/bioroebe/sequence/protein.rb +105 -3
  126. data/lib/bioroebe/sequence/sequence.rb +61 -2
  127. data/lib/bioroebe/shell/menu.rb +3819 -3713
  128. data/lib/bioroebe/shell/misc.rb +51 -4311
  129. data/lib/bioroebe/shell/readline/readline.rb +1 -1
  130. data/lib/bioroebe/shell/shell.rb +11250 -28
  131. data/lib/bioroebe/siRNA/siRNA.rb +81 -1
  132. data/lib/bioroebe/string_matching/find_longest_substring.rb +3 -2
  133. data/lib/bioroebe/string_matching/hamming_distance.rb +1 -9
  134. data/lib/bioroebe/taxonomy/class_methods.rb +3 -8
  135. data/lib/bioroebe/taxonomy/constants.rb +4 -3
  136. data/lib/bioroebe/taxonomy/edit.rb +2 -1
  137. data/lib/bioroebe/taxonomy/help/help.rb +10 -10
  138. data/lib/bioroebe/taxonomy/info/check_available.rb +15 -9
  139. data/lib/bioroebe/taxonomy/info/info.rb +18 -11
  140. data/lib/bioroebe/taxonomy/info/is_dna.rb +46 -36
  141. data/lib/bioroebe/taxonomy/interactive.rb +140 -104
  142. data/lib/bioroebe/taxonomy/menu.rb +27 -18
  143. data/lib/bioroebe/taxonomy/parse_fasta.rb +3 -1
  144. data/lib/bioroebe/taxonomy/shared.rb +1 -0
  145. data/lib/bioroebe/taxonomy/taxonomy.rb +1 -0
  146. data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +31 -24
  147. data/lib/bioroebe/toplevel_methods/colourize_related_methods.rb +164 -0
  148. data/lib/bioroebe/toplevel_methods/databases.rb +1 -1
  149. data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +107 -63
  150. data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +14 -2
  151. data/lib/bioroebe/toplevel_methods/misc.rb +118 -11
  152. data/lib/bioroebe/toplevel_methods/nucleotides.rb +22 -5
  153. data/lib/bioroebe/toplevel_methods/open_in_browser.rb +2 -0
  154. data/lib/bioroebe/toplevel_methods/palindromes.rb +1 -2
  155. data/lib/bioroebe/toplevel_methods/taxonomy.rb +2 -2
  156. data/lib/bioroebe/toplevel_methods/to_camelcase.rb +5 -0
  157. data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +1 -9
  158. data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +1 -9
  159. data/lib/bioroebe/utility_scripts/compacter.rb +1 -9
  160. data/lib/bioroebe/utility_scripts/compseq/compseq.rb +1 -9
  161. data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +1 -9
  162. data/lib/bioroebe/utility_scripts/dot_alignment.rb +1 -9
  163. data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +1 -4
  164. data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -5
  165. data/lib/bioroebe/utility_scripts/showorf/reset.rb +1 -4
  166. data/lib/bioroebe/version/version.rb +2 -2
  167. data/lib/bioroebe/www/embeddable_interface.rb +101 -52
  168. data/lib/bioroebe/www/sinatra/sinatra.rb +186 -70
  169. data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +2 -2
  170. data/lib/bioroebe/yaml/configuration/browser.yml +1 -1
  171. data/lib/bioroebe/yaml/genomes/README.md +3 -4
  172. data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +3 -3
  173. metadata +69 -64
  174. data/doc/setup.rb +0 -1655
  175. data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +0 -50
  176. data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +0 -86
  177. data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +0 -117
  178. data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +0 -981
  179. data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +0 -156
  180. data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +0 -128
  181. data/lib/bioroebe/genbank/genbank_parser.rb +0 -291
  182. data/lib/bioroebe/java/bioroebe/Base.class +0 -0
  183. data/lib/bioroebe/java/bioroebe/Codons.java +0 -22
  184. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.class +0 -0
  185. data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java +0 -19
  186. data/lib/bioroebe/java/bioroebe.jar +0 -0
  187. data/lib/bioroebe/shell/add.rb +0 -108
  188. data/lib/bioroebe/shell/assign.rb +0 -360
  189. data/lib/bioroebe/shell/chop_and_cut.rb +0 -281
  190. data/lib/bioroebe/shell/constants.rb +0 -166
  191. data/lib/bioroebe/shell/download.rb +0 -335
  192. data/lib/bioroebe/shell/enable_and_disable.rb +0 -158
  193. data/lib/bioroebe/shell/enzymes.rb +0 -310
  194. data/lib/bioroebe/shell/fasta.rb +0 -345
  195. data/lib/bioroebe/shell/gtk.rb +0 -76
  196. data/lib/bioroebe/shell/history.rb +0 -132
  197. data/lib/bioroebe/shell/initialize.rb +0 -217
  198. data/lib/bioroebe/shell/loop.rb +0 -74
  199. data/lib/bioroebe/shell/prompt.rb +0 -107
  200. data/lib/bioroebe/shell/random.rb +0 -289
  201. data/lib/bioroebe/shell/reset.rb +0 -335
  202. data/lib/bioroebe/shell/scan_and_parse.rb +0 -135
  203. data/lib/bioroebe/shell/search.rb +0 -337
  204. data/lib/bioroebe/shell/sequences.rb +0 -200
  205. data/lib/bioroebe/shell/show_report_and_display.rb +0 -2901
  206. data/lib/bioroebe/shell/startup.rb +0 -127
  207. data/lib/bioroebe/shell/taxonomy.rb +0 -14
  208. data/lib/bioroebe/shell/tk.rb +0 -23
  209. data/lib/bioroebe/shell/user_input.rb +0 -88
  210. data/lib/bioroebe/shell/xorg.rb +0 -45
metadata CHANGED
@@ -1,14 +1,14 @@
1
1
  --- !ruby/object:Gem::Specification
2
2
  name: bioroebe
3
3
  version: !ruby/object:Gem::Version
4
- version: 0.10.80
4
+ version: 0.11.32
5
5
  platform: ruby
6
6
  authors:
7
7
  - Robert A. Heiler
8
8
  autorequire:
9
9
  bindir: bin
10
10
  cert_chain: []
11
- date: 2022-06-24 00:00:00.000000000 Z
11
+ date: 2022-09-25 00:00:00.000000000 Z
12
12
  dependencies:
13
13
  - !ruby/object:Gem::Dependency
14
14
  name: chemistry_paradise
@@ -94,8 +94,8 @@ dependencies:
94
94
  - - ">="
95
95
  - !ruby/object:Gem::Version
96
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  version: '0'
97
- description: "\nWelcome to the bioroebe-0.10.x release series! It is recommended to\nuse
98
- ruby 3.x for this series, as it is the most tested version of \nruby in regards
97
+ description: "\nWelcome to the bioroebe-0.11.x release series! It is recommended\nto
98
+ use ruby 3.x for this series, as it is the most tested version\nof ruby in regards
99
99
  to this project.\n\nThe bioroebe-project is a software suite focusing on bio-related\nlife
100
100
  sciences in general - in particular molecular biology, molecular\ngenetics, bioinformatics,
101
101
  biotechnology, system biology, synthetic\nbiology and related topics close to the
@@ -294,7 +294,6 @@ files:
294
294
  - doc/quality_control/README.md
295
295
  - doc/quality_control/commandline_applications.md
296
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  - doc/resources.md
297
- - doc/setup.rb
298
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  - doc/statistics/statistics.md
299
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  - doc/todo/README.md
300
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  - doc/todo/bioroebe_GUI_todo.md
@@ -430,11 +429,15 @@ files:
430
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  - lib/bioroebe/count/count_amount_of_nucleotides.rb
431
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  - lib/bioroebe/count/count_at.rb
432
431
  - lib/bioroebe/count/count_gc.rb
432
+ - lib/bioroebe/crystal/README.md
433
+ - lib/bioroebe/crystal/to_rna.cr
433
434
  - lib/bioroebe/css/README.md
434
435
  - lib/bioroebe/css/project.css
435
436
  - lib/bioroebe/data/README.md
436
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  - lib/bioroebe/data/bam/README.md
437
438
  - lib/bioroebe/data/data.txt
439
+ - lib/bioroebe/data/electron_microscopy/pos_example.pos
440
+ - lib/bioroebe/data/electron_microscopy/test_particles.star
438
441
  - lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta
439
442
  - lib/bioroebe/data/fasta/alu_elements.fasta
440
443
  - lib/bioroebe/data/fasta/lady_slippers_orchid.fasta
@@ -466,7 +469,9 @@ files:
466
469
  - lib/bioroebe/dotplots/advanced_dotplot.rb
467
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  - lib/bioroebe/dotplots/dotplot.rb
468
471
  - lib/bioroebe/electron_microscopy/coordinate_analyzer.rb
472
+ - lib/bioroebe/electron_microscopy/electron_microscopy_module.rb
469
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  - lib/bioroebe/electron_microscopy/fix_pos_file.rb
474
+ - lib/bioroebe/electron_microscopy/flipy.rb
470
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  - lib/bioroebe/electron_microscopy/generate_em2em_file.rb
471
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  - lib/bioroebe/electron_microscopy/parse_coordinates.rb
472
477
  - lib/bioroebe/electron_microscopy/read_file_xmd.rb
@@ -497,16 +502,10 @@ files:
497
502
  - lib/bioroebe/fasta_and_fastq/fasta_defline/README.md
498
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  - lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb
499
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  - lib/bioroebe/fasta_and_fastq/fasta_parser.rb
505
+ - lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb
500
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  - lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb
501
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  - lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb
502
- - lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb
503
- - lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb
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- - lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb
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- - lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb
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  - lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb
507
- - lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb
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- - lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb
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- - lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb
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  - lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb
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  - lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb
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  - lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb
@@ -519,12 +518,14 @@ files:
519
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  - lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb
520
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  - lib/bioroebe/genbank/README.md
521
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  - lib/bioroebe/genbank/genbank_flat_file_format_generator.rb
522
- - lib/bioroebe/genbank/genbank_parser.rb
523
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  - lib/bioroebe/gene/gene.rb
522
+ - lib/bioroebe/genome/README.md
523
+ - lib/bioroebe/genome/genome.rb
524
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  - lib/bioroebe/genomes/genome_pattern.rb
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  - lib/bioroebe/genomes/genome_retriever.rb
526
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  - lib/bioroebe/gui/experimental/README.md
527
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  - lib/bioroebe/gui/experimental/snapgene/snapgene.rb
528
+ - lib/bioroebe/gui/gtk
528
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  - lib/bioroebe/gui/gtk3/README.md
529
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  - lib/bioroebe/gui/gtk3/alignment/alignment.rb
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  - lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb
@@ -582,6 +583,10 @@ files:
582
583
  - lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb
583
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  - lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb
584
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  - lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb
586
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne$1.class
587
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne$CloseListener.class
588
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne.class
589
+ - lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java
585
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  - lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb
586
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  - lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb
587
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  - lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb
@@ -604,40 +609,45 @@ files:
604
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  - lib/bioroebe/images/small_DNA_logo.png
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  - lib/bioroebe/images/small_drosophila_image.png
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  - lib/bioroebe/java/README.md
607
- - lib/bioroebe/java/bioroebe.jar
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  - lib/bioroebe/java/bioroebe/AllInOne.class
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  - lib/bioroebe/java/bioroebe/AllInOne.java
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- - lib/bioroebe/java/bioroebe/Base.class
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- - lib/bioroebe/java/bioroebe/Base.java
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- - lib/bioroebe/java/bioroebe/BisulfiteTreatment.class
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- - lib/bioroebe/java/bioroebe/BisulfiteTreatment.java
614
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  - lib/bioroebe/java/bioroebe/Cat.class
615
- - lib/bioroebe/java/bioroebe/Codons.class
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- - lib/bioroebe/java/bioroebe/Codons.java
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- - lib/bioroebe/java/bioroebe/Esystem.class
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- - lib/bioroebe/java/bioroebe/Esystem.java
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  - lib/bioroebe/java/bioroebe/GUI/BaseFrame.class
620
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  - lib/bioroebe/java/bioroebe/GUI/BaseFrame.java
621
- - lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.class
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- - lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java
623
- - lib/bioroebe/java/bioroebe/IsPalindrome.class
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- - lib/bioroebe/java/bioroebe/IsPalindrome.java
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- - lib/bioroebe/java/bioroebe/PartnerNucleotide.class
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- - lib/bioroebe/java/bioroebe/PartnerNucleotide.java
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  - lib/bioroebe/java/bioroebe/README.md
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- - lib/bioroebe/java/bioroebe/RemoveFile.class
629
- - lib/bioroebe/java/bioroebe/RemoveFile.java
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- - lib/bioroebe/java/bioroebe/RemoveNumbers.class
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- - lib/bioroebe/java/bioroebe/RemoveNumbers.java
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  - lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.class
633
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  - lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java
634
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  - lib/bioroebe/java/bioroebe/SaveFile.java
635
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  - lib/bioroebe/java/bioroebe/Sequence.java
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- - lib/bioroebe/java/bioroebe/ToCamelcase.class
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- - lib/bioroebe/java/bioroebe/ToCamelcase.java
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  - lib/bioroebe/java/bioroebe/ToplevelMethods.class
639
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  - lib/bioroebe/java/bioroebe/ToplevelMethods.java
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  - lib/bioroebe/java/bioroebe/enums/DNA.java
625
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.class
626
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Base.java
627
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/BisulfiteTreatment.class
628
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/BisulfiteTreatment.java
629
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.class
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+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java
631
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.class
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+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java
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+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Esystem.class
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+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Esystem.java
635
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/GenerateRandomDnaSequence.class
636
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/GenerateRandomDnaSequence.java
637
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/IsPalindrome.class
638
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/IsPalindrome.java
639
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.class
640
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java
641
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveFile.class
642
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveFile.java
643
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveNumbers.class
644
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/RemoveNumbers.java
645
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToCamelcase.class
646
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToCamelcase.java
647
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.class
648
+ - lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java
649
+ - lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.class
650
+ - lib/bioroebe/java/bioroebe/toplevel_methods/BaseComposition.java
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  - lib/bioroebe/matplotlib/matplotlib_generator.rb
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  - lib/bioroebe/misc/quiz/README.md
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  - lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb
@@ -677,6 +687,24 @@ files:
677
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  - lib/bioroebe/project/project.rb
678
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  - lib/bioroebe/protein_structure/alpha_helix.rb
679
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  - lib/bioroebe/protein_structure/helical_wheel.rb
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+ - lib/bioroebe/python/README.md
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+ - lib/bioroebe/python/__pycache__/mymodule.cpython-39.pyc
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+ - lib/bioroebe/python/gui/gtk3/all_in_one.css
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+ - lib/bioroebe/python/gui/gtk3/all_in_one.py
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+ - lib/bioroebe/python/gui/gtk3/widget1.py
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+ - lib/bioroebe/python/gui/tkinter/all_in_one.py
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+ - lib/bioroebe/python/mymodule.py
697
+ - lib/bioroebe/python/protein_to_dna.py
698
+ - lib/bioroebe/python/shell/shell.py
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+ - lib/bioroebe/python/to_rna.py
700
+ - lib/bioroebe/python/toplevel_methods/esystem.py
701
+ - lib/bioroebe/python/toplevel_methods/open_in_browser.py
702
+ - lib/bioroebe/python/toplevel_methods/palindromes.py
703
+ - lib/bioroebe/python/toplevel_methods/rds.py
704
+ - lib/bioroebe/python/toplevel_methods/shuffleseq.py
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+ - lib/bioroebe/python/toplevel_methods/three_delimiter.py
706
+ - lib/bioroebe/python/toplevel_methods/time_and_date.py
707
+ - lib/bioroebe/python/toplevel_methods/to_camelcase.py
680
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  - lib/bioroebe/raw_sequence/README.md
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  - lib/bioroebe/raw_sequence/raw_sequence.rb
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  - lib/bioroebe/readline/README.md
@@ -719,41 +747,17 @@ files:
719
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  - lib/bioroebe/sequence/protein.rb
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  - lib/bioroebe/sequence/reverse_complement.rb
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  - lib/bioroebe/sequence/sequence.rb
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- - lib/bioroebe/shell/add.rb
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- - lib/bioroebe/shell/assign.rb
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- - lib/bioroebe/shell/chop_and_cut.rb
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  - lib/bioroebe/shell/colours/colours.rb
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  - lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml
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  - lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml
728
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  - lib/bioroebe/shell/configuration/upcase_nucleotides.yml
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  - lib/bioroebe/shell/configuration/use_silent_startup.yml
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- - lib/bioroebe/shell/constants.rb
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- - lib/bioroebe/shell/download.rb
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- - lib/bioroebe/shell/enable_and_disable.rb
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- - lib/bioroebe/shell/enzymes.rb
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- - lib/bioroebe/shell/fasta.rb
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- - lib/bioroebe/shell/gtk.rb
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  - lib/bioroebe/shell/help/class.rb
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  - lib/bioroebe/shell/help/help.rb
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- - lib/bioroebe/shell/history.rb
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- - lib/bioroebe/shell/initialize.rb
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- - lib/bioroebe/shell/loop.rb
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  - lib/bioroebe/shell/menu.rb
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  - lib/bioroebe/shell/misc.rb
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- - lib/bioroebe/shell/prompt.rb
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- - lib/bioroebe/shell/random.rb
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  - lib/bioroebe/shell/readline/readline.rb
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- - lib/bioroebe/shell/reset.rb
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- - lib/bioroebe/shell/scan_and_parse.rb
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- - lib/bioroebe/shell/search.rb
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- - lib/bioroebe/shell/sequences.rb
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  - lib/bioroebe/shell/shell.rb
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- - lib/bioroebe/shell/show_report_and_display.rb
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- - lib/bioroebe/shell/startup.rb
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- - lib/bioroebe/shell/taxonomy.rb
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- - lib/bioroebe/shell/tk.rb
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- - lib/bioroebe/shell/user_input.rb
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- - lib/bioroebe/shell/xorg.rb
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  - lib/bioroebe/siRNA/README.md
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  - lib/bioroebe/siRNA/siRNA.rb
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  - lib/bioroebe/string_matching/README.md
@@ -796,6 +800,7 @@ files:
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  - lib/bioroebe/toplevel_methods/cat.rb
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  - lib/bioroebe/toplevel_methods/chunked_display.rb
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  - lib/bioroebe/toplevel_methods/cliner.rb
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+ - lib/bioroebe/toplevel_methods/colourize_related_methods.rb
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  - lib/bioroebe/toplevel_methods/complement.rb
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  - lib/bioroebe/toplevel_methods/convert_global_env.rb
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  - lib/bioroebe/toplevel_methods/databases.rb
@@ -1025,7 +1030,7 @@ post_install_message: |2+
1025
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1026
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  For more documentation, have a look at:
1027
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1028
- https://www.rubydoc.info/gems/bioroebe/0.10.80
1033
+ https://www.rubydoc.info/gems/bioroebe/0.11.32
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1030
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  rdoc_options: []
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  require_paths:
@@ -1034,18 +1039,18 @@ required_ruby_version: !ruby/object:Gem::Requirement
1034
1039
  requirements:
1035
1040
  - - ">="
1036
1041
  - !ruby/object:Gem::Version
1037
- version: 2.5.8
1042
+ version: 2.7.6
1038
1043
  required_rubygems_version: !ruby/object:Gem::Requirement
1039
1044
  requirements:
1040
1045
  - - ">="
1041
1046
  - !ruby/object:Gem::Version
1042
- version: 3.3.16
1047
+ version: 3.3.22
1043
1048
  requirements: []
1044
- rubygems_version: 3.3.16
1049
+ rubygems_version: 3.3.22
1045
1050
  signing_key:
1046
1051
  specification_version: 4
1047
- summary: 'Welcome to the bioroebe-0.10.x release series! It is recommended to use
1048
- ruby 3.x for this series, as it is the most tested version of ruby in regards to
1052
+ summary: 'Welcome to the bioroebe-0.11.x release series! It is recommended to use
1053
+ ruby 3.x for this series, as it is the most tested version of ruby in regards to
1049
1054
  this project. The bioroebe-project is a software suite focusing on bio-related
1050
1055
  life sciences in general - in particular molecular biology, molecular genetics,
1051
1056
  bioinformatics, biotechnology, system biology, synthetic biology and related topics