bioroebe 0.12.24 → 0.13.31
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- checksums.yaml +4 -4
- data/LICENSE.md +7 -8
- data/README.md +566 -354
- data/bin/all_positions_of_this_nucleotide +1 -1
- data/bin/aminoacid_frequencies +1 -1
- data/bin/automatically_rename_this_fasta_file +1 -1
- data/bin/base_composition +1 -1
- data/bin/batch_create_windows_executables +1 -1
- data/bin/bioroebe +12 -1
- data/bin/bioroebe_cat +7 -0
- data/bin/calculate_exponential_growth +7 -0
- data/bin/calculate_n50_value +1 -1
- data/bin/calculate_the_frequencies_of_this_species +7 -0
- data/bin/chunked_display +1 -1
- data/bin/codon_frequency +1 -1
- data/bin/codon_to_aminoacid +1 -1
- data/bin/colourize_this_fasta_sequence +1 -1
- data/bin/complementary_dna_strand +1 -1
- data/bin/complementary_rna_strand +1 -1
- data/bin/consensus_sequence +1 -1
- data/bin/dna_to_rna +1 -1
- data/bin/downcase_chunked_display +1 -1
- data/bin/download_this_pdb +1 -1
- data/bin/fasta_index +1 -1
- data/bin/fetch_data_from_uniprot +1 -1
- data/bin/filter_away_invalid_nucleotides +1 -1
- data/bin/find_substring +1 -1
- data/bin/input_as_dna +1 -1
- data/bin/is_palindrome +1 -1
- data/bin/leading_five_prime +1 -1
- data/bin/longest_ORF +1 -1
- data/bin/longest_substring +1 -1
- data/bin/open_reading_frames +1 -1
- data/bin/partner_nucleotide +1 -1
- data/bin/plain_palindrome +1 -1
- data/bin/random_dna_sequence +1 -1
- data/bin/random_sequence +1 -1
- data/bin/raw_hamming_distance +1 -1
- data/bin/return_longest_substring_via_LCS_algorithm +1 -1
- data/bin/reverse_sequence +1 -1
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +1 -1
- data/bin/show_atomic_composition +1 -1
- data/bin/show_fasta_header +1 -1
- data/bin/show_nucleotide_sequence +1 -1
- data/bin/show_this_dna_sequence +1 -1
- data/bin/show_time_now +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +1 -1
- data/bin/strict_filter_away_invalid_aminoacids +1 -1
- data/{lib/bioroebe/base/reset.rb → bin/three_delimiter} +9 -6
- data/bin/three_to_one +1 -1
- data/bin/to_rna +1 -1
- data/bin/trailing_three_prime +1 -1
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +1 -1
- data/bioroebe.gemspec +6 -7
- data/doc/README.gen +534 -322
- data/doc/blosum/blosum.md +4 -0
- data/doc/compatibility/BIO_PHP.md +20 -18
- data/doc/compatibility/README.md +2 -3
- data/doc/compatibility/emboss.md +5 -3
- data/doc/{extensive_usage_example.md → extensive_usage_example/extensive_usage_example.md} +4 -2
- data/doc/{instructions_for_the_taxonomy_subproject.md → instructions_for_the_taxonomy_subproject/instructions_for_the_taxonomy_subproject.md} +36 -33
- data/doc/{legacy_paths.md → legacy_paths/legacy_paths.md} +3 -3
- data/doc/statistics/statistics.md +12 -10
- data/doc/todo/bioroebe_GUI_todo.md +6 -1
- data/doc/todo/bioroebe_java_todo.md +3 -2
- data/doc/todo/bioroebe_todo.md +328 -310
- data/doc/{using_biomart.md → using_biomart/using_biomart.md} +7 -3
- data/lib/bioroebe/abstract/features.rb +0 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +1 -1
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +3 -1
- data/lib/bioroebe/aminoacids/codon_percentage.rb +18 -10
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +5 -2
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +90 -64
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +1 -3
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +2 -2
- data/lib/bioroebe/annotations/create_annotation_format.rb +2 -2
- data/lib/bioroebe/base/base.rb +101 -6
- data/lib/bioroebe/base/base_module/base_module.rb +9 -1
- data/lib/bioroebe/base/colours.rb +3 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +80 -44
- data/lib/bioroebe/base/commandline_application/README.md +1 -1
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +661 -22
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +2 -1
- data/lib/bioroebe/base/infer_the_namespace_module/infer_the_namespace_module.rb +37 -0
- data/lib/bioroebe/base/internal_hash_module/internal_hash_module.rb +1 -6
- data/lib/bioroebe/base/prototype/prototype.rb +155 -14
- data/lib/bioroebe/biomart/attribute.rb +1 -1
- data/lib/bioroebe/biomart/biomart.rb +8 -9
- data/lib/bioroebe/biomart/server.rb +1 -1
- data/lib/bioroebe/blosum/blosum.rb +2 -2
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +5 -3
- data/lib/bioroebe/calculate/calculate_gc_content.rb +1 -1
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +5 -3
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +2 -10
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +6 -15
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +4 -2
- data/lib/bioroebe/cell/cell.rb +3 -2
- data/lib/bioroebe/cell/specialized_cells/B_cell.rb +60 -0
- data/lib/bioroebe/cell/specialized_cells/Macrophage.rb +60 -0
- data/lib/bioroebe/cell/specialized_cells/README.md +5 -0
- data/lib/bioroebe/cell/specialized_cells/T_cell.rb +60 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +3 -1
- data/lib/bioroebe/cleave_and_digest/digestion.rb +1 -1
- data/lib/bioroebe/codon_tables/frequencies/10090_Mus_musculus.yml +93 -0
- data/lib/bioroebe/codon_tables/frequencies/107243_Thlaspi_caerulescens.yml +72 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +2 -2
- data/lib/bioroebe/codons/codon_table.rb +10 -2
- data/lib/bioroebe/codons/codons.rb +3 -3
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +18 -15
- data/lib/bioroebe/codons/determine_optimal_codons.rb +1 -1
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +4 -2
- data/lib/bioroebe/codons/show_codon_tables.rb +1 -1
- data/lib/bioroebe/codons/show_codon_usage.rb +1 -2
- data/lib/bioroebe/codons/show_this_codon_table.rb +2 -2
- data/lib/bioroebe/codons/start_codons.rb +7 -3
- data/lib/bioroebe/colours/colour_schemes/README.md +1 -1
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +3 -3
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +3 -3
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +4 -3
- data/lib/bioroebe/colours/colour_schemes/helix.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/score.rb +13 -2
- data/lib/bioroebe/colours/colour_schemes/strand.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/turn.rb +3 -1
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +1 -1
- data/lib/bioroebe/{toplevel_methods/colourize_related_methods.rb → colours/colourize_related_code.rb} +1 -3
- data/lib/bioroebe/colours/colourize_sequence.rb +3 -1
- data/lib/bioroebe/colours/colours.rb +172 -15
- data/lib/bioroebe/configuration/configuration.rb +1 -1
- data/lib/bioroebe/constants/GUIs.rb +2 -2
- data/lib/bioroebe/constants/constants.rb +1349 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +8 -13
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +9 -3
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +11 -10
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +1 -1
- data/lib/bioroebe/count/count_at.rb +2 -1
- data/lib/bioroebe/databases/download_taxonomy_database.rb +1 -1
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +2 -2
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +2 -2
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +2 -2
- data/lib/bioroebe/electron_microscopy/flipy.rb +2 -2
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +3 -11
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +6 -6
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +6 -6
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +2 -2
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +1 -1
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +1 -1
- data/lib/bioroebe/enzymes/restriction_enzymes/statistics.rb +4 -3
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +1 -1
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +4 -3
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +3 -3
- data/lib/bioroebe/ext/main.cpp +0 -1
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +3 -3
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +8 -14
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/fasta_to_yaml/fasta_to_yaml.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +37 -11
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +2 -2
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +5 -13
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +1 -1
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +3 -6
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +3 -3
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +20 -11
- data/lib/bioroebe/genome/genome.rb +1 -1
- data/lib/bioroebe/genomes/genome_pattern.rb +17 -16
- data/lib/bioroebe/genomes/genome_retriever.rb +4 -2
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +10 -13
- data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb +557 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/aminoacid_composition.rb +498 -198
- data/lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb +665 -0
- data/lib/bioroebe/gui/universal_widgets/blosum_matrix_viewer/blosum_matrix_viewer.rb +329 -0
- data/lib/bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +423 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/controller/controller.rb +170 -118
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +277 -215
- 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
- data/lib/bioroebe/gui/universal_widgets/fasta_table_widget/fasta_table_widget.rb +643 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/format_converter/format_converter.rb +236 -164
- data/lib/bioroebe/gui/universal_widgets/gene/gene.rb +278 -0
- data/lib/bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb +646 -0
- data/lib/bioroebe/gui/{shared_code/levensthein_distance/levensthein_distance_module.rb → universal_widgets/levensthein_distance/levensthein_distance.rb} +313 -88
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/nucleotide_analyser/nucleotide_analyser.rb +281 -189
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/parse_pdb_file/parse_pdb_file.rb +265 -149
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/primer_design_widget/primer_design_widget.rb +337 -263
- data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb +408 -0
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/random_sequence/random_sequence.rb +245 -187
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.rb +207 -137
- data/lib/bioroebe/gui/universal_widgets/shell/shell.rb +288 -0
- data/lib/bioroebe/gui/{gtk3/show_codon_table/misc.rb → universal_widgets/show_codon_table/show_codon_table.rb} +290 -110
- 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
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/sizeseq/sizeseq.rb +151 -69
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/three_to_one/three_to_one.rb +190 -127
- data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.rb +211 -152
- data/lib/bioroebe/images/images.html +953 -1170
- data/lib/bioroebe/images/misc/README.md +6 -0
- data/lib/bioroebe/images/misc/activation.avif +0 -0
- data/lib/bioroebe/images/misc/inhibition.avif +0 -0
- data/lib/bioroebe/images/misc/small_virus_logo.avif +0 -0
- data/lib/bioroebe/{constants/base_directory.rb → log_directory/log_directory.rb} +79 -59
- data/lib/bioroebe/matplotlib/matplotlib_generator.rb +1 -1
- data/lib/bioroebe/misc/quiz/three_letter_to_aminoacid.rb +1 -1
- data/lib/bioroebe/misc/ruler.rb +5 -5
- data/lib/bioroebe/misc/useful_formulas.rb +3 -3
- data/lib/bioroebe/ncbi/efetch.rb +1 -2
- data/lib/bioroebe/ngs/phred_quality_score_table.rb +3 -3
- data/lib/bioroebe/nucleotides/complementary_dna_strand.rb +3 -6
- data/lib/bioroebe/nucleotides/molecular_weight_of_nucleotides.rb +3 -3
- data/lib/bioroebe/nucleotides/most_likely_nucleotide_sequence_for_this_aminoacid_sequence.rb +6 -10
- data/lib/bioroebe/nucleotides/{show_nucleotide_sequence.rb → show_nucleotide_sequence/show_nucleotide_sequence.rb} +377 -255
- data/lib/bioroebe/palindromes/palindrome_2D_structure.rb +1 -1
- data/lib/bioroebe/palindromes/palindrome_finder.rb +1 -1
- data/lib/bioroebe/palindromes/palindrome_generator.rb +2 -10
- data/lib/bioroebe/parsers/biolang_parser.rb +1 -1
- data/lib/bioroebe/parsers/blosum_parser.rb +14 -19
- data/lib/bioroebe/parsers/genbank_parser.rb +2 -6
- data/lib/bioroebe/parsers/gff.rb +9 -9
- data/lib/bioroebe/parsers/parse_embl.rb +2 -6
- data/lib/bioroebe/parsers/stride_parser.rb +4 -12
- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +2 -2
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +6 -3
- data/lib/bioroebe/patterns/profile_pattern.rb +2 -2
- data/lib/bioroebe/patterns/rgg_scanner.rb +4 -2
- data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/alpha_helix.rb +2 -2
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/download_this_pdb.rb +2 -3
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/fetch_fasta_sequence_from_pdb.rb +4 -4
- data/lib/bioroebe/{protein_structure → pdb_and_protein_structure}/helical_wheel.rb +2 -2
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_mmCIF_file.rb +1 -1
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/parse_pdb_file.rb +3 -3
- data/lib/bioroebe/{pdb → pdb_and_protein_structure}/report_secondary_structures_from_this_pdb_file.rb +3 -3
- data/lib/bioroebe/project/project.rb +3 -1
- data/lib/bioroebe/raw_sequence/README.md +8 -8
- data/lib/bioroebe/raw_sequence/raw_sequence.rb +11 -2
- data/lib/bioroebe/regexes/regexes.rb +1 -2
- data/lib/bioroebe/requires/commandline_application.rb +3 -1
- data/lib/bioroebe/requires/require_all_pdb_files.rb +1 -1
- data/lib/bioroebe/requires/require_all_taxonomy_files.rb +1 -1
- data/lib/bioroebe/requires/require_all_utility_scripts_files.rb +10 -0
- data/lib/bioroebe/requires/require_colours.rb +1 -1
- data/lib/bioroebe/requires/require_the_bioroebe_project.rb +5 -7
- data/lib/bioroebe/requires/require_the_bioroebe_sinatra_components.rb +1 -1
- data/lib/bioroebe/requires/require_the_constants.rb +2 -14
- data/lib/bioroebe/requires/require_yaml.rb +7 -5
- data/lib/bioroebe/sequence/alignment.rb +1 -1
- data/lib/bioroebe/sequence/dna.rb +4 -2
- data/lib/bioroebe/sequence/nucleotide_module/nucleotide_module.rb +22 -8
- data/lib/bioroebe/sequence/protein.rb +2 -2
- data/lib/bioroebe/sequence/reverse_complement.rb +3 -3
- data/lib/bioroebe/sequence/rna.rb +9 -8
- data/lib/bioroebe/sequence/sequence.rb +3 -3
- data/lib/bioroebe/shell/configuration/additionally_set_xorg_buffer.yml +0 -0
- data/lib/bioroebe/shell/configuration/may_we_show_the_startup_information.yml +0 -0
- data/lib/bioroebe/shell/configuration/upcase_nucleotides.yml +0 -0
- data/lib/bioroebe/shell/configuration/use_silent_startup.yml +1 -1
- data/lib/bioroebe/shell/help/class.rb +68 -19
- data/lib/bioroebe/shell/menu.rb +5244 -5322
- data/lib/bioroebe/shell/{readline/readline.rb → readline.rb} +1 -3
- data/lib/bioroebe/shell/shell.rb +11240 -453
- data/lib/bioroebe/siRNA/siRNA.rb +3 -3
- data/lib/bioroebe/{gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb → sinatra/sinatra_interface.rb} +28 -19
- data/lib/bioroebe/{www/sinatra/sinatra.rb → sinatra/sinatra_wrapper.rb} +731 -754
- data/lib/bioroebe/string_matching/find_longest_substring.rb +2 -10
- data/lib/bioroebe/string_matching/find_longest_substring_via_LCS_algorithm.rb +4 -14
- data/lib/bioroebe/string_matching/hamming_distance.rb +11 -10
- data/lib/bioroebe/string_matching/levensthein.rb +5 -17
- data/lib/bioroebe/string_matching/simple_string_comparer.rb +48 -4
- data/lib/bioroebe/string_matching/smith_waterman.rb +11 -6
- data/lib/bioroebe/svg/glyph.rb +4 -1
- data/lib/bioroebe/svg/mini_feature.rb +1 -1
- data/lib/bioroebe/svg/page.rb +18 -7
- data/lib/bioroebe/svg/svgee.rb +22 -13
- data/lib/bioroebe/svg/track.rb +20 -4
- data/lib/bioroebe/taxonomy/chart.rb +2 -2
- data/lib/bioroebe/taxonomy/class_methods.rb +5 -6
- data/lib/bioroebe/taxonomy/constants.rb +1 -1
- data/lib/bioroebe/taxonomy/info/info.rb +1 -1
- data/lib/bioroebe/taxonomy/info/is_dna.rb +1 -1
- data/lib/bioroebe/taxonomy/interactive.rb +1 -2
- data/lib/bioroebe/taxonomy/menu.rb +1 -1
- data/lib/bioroebe/taxonomy/node.rb +1 -1
- data/lib/bioroebe/taxonomy/parse_fasta.rb +4 -2
- data/lib/bioroebe/taxonomy/shared.rb +5 -4
- data/lib/bioroebe/taxonomy/taxonomy.rb +2 -4
- data/lib/bioroebe/toplevel_methods/fasta_and_fastq.rb +3 -45
- data/lib/bioroebe/toplevel_methods/{is_on_roebe.rb → roebe.rb} +1 -11
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +6 -12
- data/lib/bioroebe/toplevel_methods/toplevel_methods.rb +5568 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +4 -3
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +2 -2
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +16 -9
- data/lib/bioroebe/utility_scripts/compacter/compacter.rb +4 -2
- data/lib/bioroebe/utility_scripts/compare_these_two_sequences_via_blosum.rb +119 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +11 -9
- data/lib/bioroebe/utility_scripts/{consensus_sequence.rb → consensus_sequence/consensus_sequence.rb} +13 -4
- data/lib/bioroebe/utility_scripts/{create_batch_entrez_file.rb → create_batch_entrez_file/create_batch_entrez_file.rb} +5 -5
- data/lib/bioroebe/utility_scripts/{determine_antigenic_areas.rb → determine_antigenic_areas/determine_antigenic_areas.rb} +5 -5
- data/lib/bioroebe/utility_scripts/{determine_missing_nucleotides_percentage.rb → determine_missing_nucleotides_percentage/determine_missing_nucleotides_percentage.rb} +16 -15
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +7 -7
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +1 -1
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +2 -0
- data/lib/bioroebe/utility_scripts/{dot_alignment.rb → dot_alignment/dot_alignment.rb} +3 -3
- data/lib/bioroebe/utility_scripts/{download_files_from_rebase.rb → download_files_from_rebase/download_files_from_rebase.rb} +5 -5
- data/lib/bioroebe/utility_scripts/fetch_data_from_uniprot/fetch_data_from_uniprot.rb +269 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +4 -2
- data/lib/bioroebe/utility_scripts/{mirror_repeat.rb → mirror_repeat/mirror_repeat.rb} +5 -5
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +3 -3
- data/lib/bioroebe/utility_scripts/{parse_taxonomy.rb → parse_taxonomy/parse_taxonomy.rb} +15 -6
- data/lib/bioroebe/utility_scripts/{pathways.rb → pathways/pathways.rb} +4 -3
- data/lib/bioroebe/utility_scripts/{permutations.rb → permutations/permutations.rb} +3 -3
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +4 -2
- data/lib/bioroebe/utility_scripts/{show_this_dna_sequence.rb → show_this_dna_sequence/show_this_dna_sequence.rb} +1 -1
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +406 -10
- data/lib/bioroebe/version/version.rb +2 -2
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +5 -13
- data/lib/bioroebe/virus/individual_viruses/README.md +15 -0
- data/lib/bioroebe/virus/individual_viruses/tobacco_mosaic_virus.rb +40 -0
- data/lib/bioroebe/virus/virus.rb +76 -0
- data/lib/bioroebe/www/bioroebe.cgi +4 -3
- data/lib/bioroebe/www/embeddable_interface.rb +85 -49
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +6 -6
- data/lib/bioroebe/yaml/antisense/antisense.yml +2 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +6 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +2 -1
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +2 -2
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -1
- data/lib/bioroebe/yaml/consensus_sequences/consensus_sequences.yml +1 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +7 -6
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +3 -3
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +1 -5
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +1 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +2 -1
- data/lib/bioroebe/yaml/promoters/35S.yml +3 -1
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -1
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -1
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +7 -7
- data/spec/testing_toplevel_method_editor.rb +1 -1
- data/spec/testing_toplevel_method_verbose.rb +1 -1
- data/test/testing_dna_to_rna_conversion.rb +1 -1
- metadata +127 -235
- data/doc/blosum.md +0 -5
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +0 -33
- data/lib/bioroebe/base/commandline_application/directory.rb +0 -33
- data/lib/bioroebe/base/commandline_application/extract.rb +0 -22
- data/lib/bioroebe/base/commandline_application/misc.rb +0 -502
- data/lib/bioroebe/base/commandline_application/opn.rb +0 -47
- data/lib/bioroebe/base/commandline_application/reset.rb +0 -42
- data/lib/bioroebe/base/commandline_application/warnings.rb +0 -36
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +0 -29
- data/lib/bioroebe/base/initialize.rb +0 -18
- data/lib/bioroebe/base/misc.rb +0 -129
- data/lib/bioroebe/base/namespace.rb +0 -16
- data/lib/bioroebe/base/prototype/e_and_ee.rb +0 -24
- data/lib/bioroebe/base/prototype/misc.rb +0 -114
- data/lib/bioroebe/base/prototype/mkdir.rb +0 -20
- data/lib/bioroebe/base/prototype/reset.rb +0 -36
- data/lib/bioroebe/colours/misc_colours.rb +0 -80
- data/lib/bioroebe/colours/rev.rb +0 -44
- data/lib/bioroebe/colours/sdir.rb +0 -21
- data/lib/bioroebe/colours/sfancy.rb +0 -21
- data/lib/bioroebe/colours/sfile.rb +0 -21
- data/lib/bioroebe/colours/simp.rb +0 -21
- data/lib/bioroebe/colours/swarn.rb +0 -29
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +0 -147
- data/lib/bioroebe/constants/carriage_return.rb +0 -14
- data/lib/bioroebe/constants/codon_tables.rb +0 -77
- data/lib/bioroebe/constants/database_constants.rb +0 -107
- data/lib/bioroebe/constants/files_and_directories.rb +0 -606
- data/lib/bioroebe/constants/misc.rb +0 -209
- data/lib/bioroebe/constants/newline.rb +0 -14
- data/lib/bioroebe/constants/nucleotides.rb +0 -121
- data/lib/bioroebe/constants/regex.rb +0 -28
- data/lib/bioroebe/constants/roebe.rb +0 -38
- data/lib/bioroebe/constants/row_terminator.rb +0 -16
- data/lib/bioroebe/constants/tabulator.rb +0 -14
- data/lib/bioroebe/constants/unicode.rb +0 -12
- data/lib/bioroebe/constants/urls.rb +0 -50
- data/lib/bioroebe/gui/gtk +0 -1
- data/lib/bioroebe/gui/gtk3/README.md +0 -2
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +0 -306
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +0 -29
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -195
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -105
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -188
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +0 -322
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +0 -181
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +0 -383
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +0 -174
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +0 -181
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +0 -101
- data/lib/bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb +0 -145
- data/lib/bioroebe/gui/gtk3/three_to_one/title.rb +0 -23
- data/lib/bioroebe/gui/jruby/alignment/alignment.rb +0 -165
- data/lib/bioroebe/gui/jruby/aminoacid_composition/aminoacid_composition.rb +0 -166
- data/lib/bioroebe/gui/jruby/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -82
- data/lib/bioroebe/gui/libui/README.md +0 -4
- data/lib/bioroebe/gui/libui/alignment/alignment.rb +0 -116
- data/lib/bioroebe/gui/libui/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -112
- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +0 -60
- data/lib/bioroebe/gui/libui/controller/controller.rb +0 -116
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +0 -161
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +0 -76
- data/lib/bioroebe/gui/libui/hamming_distance/hamming_distance.rb +0 -135
- data/lib/bioroebe/gui/libui/levensthein_distance/levensthein_distance.rb +0 -118
- data/lib/bioroebe/gui/libui/protein_to_DNA/protein_to_DNA.rb +0 -115
- data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb +0 -190
- data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb +0 -134
- data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb +0 -89
- data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb +0 -113
- data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb +0 -102
- data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb +0 -94
- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +0 -216
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +0 -192
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +0 -72
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +0 -206
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +0 -140
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +0 -262
- data/lib/bioroebe/gui/tk/levensthein_distance/levensthein_distance.rb +0 -243
- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +0 -199
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +0 -519
- data/lib/bioroebe/shell/colours/colours.rb +0 -235
- data/lib/bioroebe/shell/help/help.rb +0 -25
- data/lib/bioroebe/shell/misc.rb +0 -10227
- data/lib/bioroebe/toplevel_methods/ad_hoc_task.rb +0 -56
- data/lib/bioroebe/toplevel_methods/aminoacids_and_proteins.rb +0 -722
- data/lib/bioroebe/toplevel_methods/atomic_composition.rb +0 -198
- data/lib/bioroebe/toplevel_methods/base_composition.rb +0 -121
- data/lib/bioroebe/toplevel_methods/blast.rb +0 -153
- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +0 -57
- data/lib/bioroebe/toplevel_methods/cat.rb +0 -71
- data/lib/bioroebe/toplevel_methods/chunked_display.rb +0 -92
- data/lib/bioroebe/toplevel_methods/cliner.rb +0 -81
- data/lib/bioroebe/toplevel_methods/complement.rb +0 -58
- data/lib/bioroebe/toplevel_methods/convert_global_env.rb +0 -39
- data/lib/bioroebe/toplevel_methods/databases.rb +0 -73
- data/lib/bioroebe/toplevel_methods/delimiter.rb +0 -19
- data/lib/bioroebe/toplevel_methods/digest.rb +0 -81
- data/lib/bioroebe/toplevel_methods/download_and_fetch_data.rb +0 -146
- data/lib/bioroebe/toplevel_methods/e.rb +0 -20
- data/lib/bioroebe/toplevel_methods/editor.rb +0 -21
- data/lib/bioroebe/toplevel_methods/esystem.rb +0 -22
- data/lib/bioroebe/toplevel_methods/exponential_growth.rb +0 -74
- data/lib/bioroebe/toplevel_methods/extract.rb +0 -56
- data/lib/bioroebe/toplevel_methods/file_and_directory_related_actions.rb +0 -269
- data/lib/bioroebe/toplevel_methods/frequencies.rb +0 -99
- data/lib/bioroebe/toplevel_methods/hamming_distance.rb +0 -60
- data/lib/bioroebe/toplevel_methods/infer.rb +0 -66
- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +0 -101
- data/lib/bioroebe/toplevel_methods/levensthein.rb +0 -63
- data/lib/bioroebe/toplevel_methods/log_directory.rb +0 -109
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +0 -55
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +0 -88
- data/lib/bioroebe/toplevel_methods/matches.rb +0 -259
- data/lib/bioroebe/toplevel_methods/misc.rb +0 -596
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +0 -787
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +0 -63
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +0 -79
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +0 -236
- data/lib/bioroebe/toplevel_methods/opn.rb +0 -34
- data/lib/bioroebe/toplevel_methods/palindromes.rb +0 -155
- data/lib/bioroebe/toplevel_methods/parse.rb +0 -59
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +0 -68
- data/lib/bioroebe/toplevel_methods/rds.rb +0 -24
- data/lib/bioroebe/toplevel_methods/remove.rb +0 -86
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +0 -35
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +0 -68
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +0 -73
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +0 -69
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +0 -116
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +0 -37
- data/lib/bioroebe/toplevel_methods/statistics.rb +0 -53
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +0 -62
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +0 -34
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +0 -53
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +0 -31
- data/lib/bioroebe/toplevel_methods/truncate.rb +0 -48
- data/lib/bioroebe/toplevel_methods/url.rb +0 -36
- data/lib/bioroebe/toplevel_methods/verbose.rb +0 -59
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +0 -31
- data/lib/bioroebe/utility_scripts/showorf/help.rb +0 -33
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +0 -52
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +0 -68
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +0 -36
- data/lib/bioroebe/utility_scripts/showorf/run.rb +0 -152
- data/lib/bioroebe/utility_scripts/showorf/show.rb +0 -97
- /data/doc/{german_names_for_the_aminoacids.md → german_names_for_the_aminoacids/german_names_for_the_aminoacids.md} +0 -0
- /data/doc/{pdb_ATOM_entry.md → pdb_ATOM_entry/pdb_ATOM_entry.md} +0 -0
- /data/doc/{resources.md → resources/resources.md} +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/aminoacid_composition/customized_dialog.rb +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/anti_sense_strand/anti_sense_strand.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/hamming_distance/hamming_distance.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/levensthein_distance/levensthein_distance.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/protein_to_DNA/protein_to_DNA.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/restriction_enzymes/restriction_enzymes.config +0 -0
- /data/lib/bioroebe/gui/{gtk3 → universal_widgets}/www_finder/www_finder.config +0 -0
- /data/lib/bioroebe/yaml/{base_composition_of_dna.yml → base_composition_of_dna/base_composition_of_dna.yml} +0 -0
- /data/lib/bioroebe/yaml/{nuclear_localization_sequences.yml → nuclear_localization_sequences/nuclear_localization_sequences.yml} +0 -0
- /data/lib/bioroebe/yaml/{talens.yml → talens/talens.yml} +0 -0
@@ -2,53 +2,78 @@
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# === USE_THIS_SLIGHTLY_SMALLER_FONT
|
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+
# ========================================================================= #
|
76
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+
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
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|
# ========================================================================= #
|
71
91
|
def initialize(
|
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|
-
commandline_arguments =
|
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+
commandline_arguments = nil,
|
73
93
|
run_already = true
|
74
94
|
)
|
75
|
-
|
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
|
# ========================================================================= #
|
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106
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def reset
|
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+
super() if respond_to?(:super)
|
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|
reset_the_internal_variables
|
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+
reset_the_base_module # This must come after reset_the_internal_variables().
|
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+
infer_the_namespace
|
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111
|
# ======================================================================= #
|
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112
|
# === @configuration
|
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113
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# ======================================================================= #
|
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|
-
@configuration = [true, __dir__,
|
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+
@configuration = [true, __dir__, namespace?]
|
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+
# ======================================================================= #
|
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+
# === Set the title, width, height and the font in use.
|
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+
# ======================================================================= #
|
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118
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title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
|
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+
handle_CSS if use_gtk3?
|
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120
|
# ======================================================================= #
|
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|
# === @list_store
|
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|
# ======================================================================= #
|
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@list_store = nil
|
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-
handle_CSS
|
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-
infer_the_size_automatically
|
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|
end
|
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125
|
|
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126
|
# ========================================================================= #
|
@@ -114,76 +138,129 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
|
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114
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|
end
|
115
139
|
|
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# ========================================================================= #
|
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-
# ===
|
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+
# === main_font?
|
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# ========================================================================= #
|
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-
def
|
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|
-
|
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|
-
end
|
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|
-
alias main_sequence? aminoacid_sequence? # === main_sequence?
|
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+
def main_font?
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+
USE_THIS_FONT
|
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+
end
|
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146
|
|
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# ========================================================================= #
|
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|
-
# ===
|
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+
# === slightly_smaller_font?
|
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149
|
# ========================================================================= #
|
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|
-
def
|
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|
-
|
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-
show_hidden: true,
|
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|
-
add_these_shortcut_folders: ::Bioroebe.log_dir?,
|
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|
-
current_folder: ::Bioroebe.log_dir?
|
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|
-
}}
|
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|
-
if File.exist? filename
|
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|
-
_ = filename
|
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|
-
if _.end_with? '.fasta'
|
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|
-
require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
|
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|
-
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
|
-
# ===
|
155
|
+
# === handle_CSS_rules (CSS tag, css tag)
|
148
156
|
# ========================================================================= #
|
149
|
-
def
|
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
|
-
#
|
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
|
-
@
|
156
|
-
|
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
|
-
# ===
|
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
|
164
|
-
|
165
|
-
|
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
|
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
|
-
|
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 =
|
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 =
|
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 =
|
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 =
|
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 =
|
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 =
|
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 =
|
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
|
-
# ===
|
514
|
+
# === run (run tag)
|
457
515
|
# ========================================================================= #
|
458
|
-
def
|
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
|
-
# ===
|
521
|
+
# === aminoacid_sequence?
|
473
522
|
# ========================================================================= #
|
474
|
-
def
|
475
|
-
|
476
|
-
|
477
|
-
|
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
|
-
# ===
|
529
|
+
# === do_open_a_file_and_then_set_the_correct_values
|
483
530
|
# ========================================================================= #
|
484
|
-
def
|
485
|
-
|
486
|
-
|
487
|
-
|
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
|
-
# ===
|
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
|
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
|
-
#
|
538
|
-
#
|
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
|
-
|
541
|
-
|
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
|
-
# ===
|
565
|
+
# === on_right_click_in_the_tree_view_deselect_the_selection
|
546
566
|
# ========================================================================= #
|
547
|
-
def
|
548
|
-
|
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.
|
614
|
+
# === Bioroebe::GUI::Gtk::RandomSequence.run
|
553
615
|
# ========================================================================= #
|
554
|
-
def self.
|
616
|
+
def self.run(
|
555
617
|
i = ARGV
|
556
618
|
)
|
557
|
-
|
558
|
-
|
559
|
-
|
560
|
-
|
561
|
-
|
562
|
-
|
563
|
-
|
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::
|
630
|
+
Bioroebe::GUI::UniversalWidgets::RandomSequence.new(ARGV)
|
573
631
|
end # gtkrandomsequence
|