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
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menu(optional_commandline_arguments)
|
92
|
-
end
|
93
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-
signal_destroy_then_quit
|
94
|
-
run if run_already
|
95
|
-
end
|
96
|
-
|
97
|
-
# ========================================================================= #
|
98
|
-
# === reset (reset tag)
|
99
|
-
# ========================================================================= #
|
100
|
-
def reset
|
101
|
-
reset_the_internal_variables
|
102
|
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# ======================================================================= #
|
103
|
-
# === @configuration
|
104
|
-
# ======================================================================= #
|
105
|
-
@configuration = [true, __dir__, NAMESPACE]
|
106
|
-
title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
|
107
|
-
use_gtk_paradise_project_CSS_file
|
108
|
-
append_project_CSS_file
|
109
|
-
set_border_width(5)
|
110
|
-
infer_the_size_automatically
|
111
|
-
end
|
112
|
-
|
113
|
-
# ========================================================================= #
|
114
|
-
# === padding?
|
115
|
-
# ========================================================================= #
|
116
|
-
def padding?
|
117
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-
PADDING_TO_USE
|
118
|
-
end
|
119
|
-
|
120
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-
# ========================================================================= #
|
121
|
-
# === border_size?
|
122
|
-
# ========================================================================= #
|
123
|
-
def border_size?
|
124
|
-
0
|
125
|
-
end
|
126
|
-
|
127
|
-
# ========================================================================= #
|
128
|
-
# === seq1?
|
129
|
-
# ========================================================================= #
|
130
|
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def seq1?
|
131
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@entry_on_top.text
|
132
|
-
end
|
133
|
-
|
134
|
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# ========================================================================= #
|
135
|
-
# === seq2?
|
136
|
-
# ========================================================================= #
|
137
|
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def seq2?
|
138
|
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@entry_on_bottom.text
|
139
|
-
end
|
140
|
-
|
141
|
-
# ========================================================================= #
|
142
|
-
# === set_minimum_size
|
143
|
-
# ========================================================================= #
|
144
|
-
def set_minimum_size
|
145
|
-
set_size_request(80, 100)
|
146
|
-
end
|
147
|
-
|
148
|
-
# ========================================================================= #
|
149
|
-
# === entry1?
|
150
|
-
# ========================================================================= #
|
151
|
-
def entry1?
|
152
|
-
@entry_on_top
|
153
|
-
end
|
154
|
-
|
155
|
-
# ========================================================================= #
|
156
|
-
# === create_entries (entries tag, entry tag)
|
157
|
-
# ========================================================================= #
|
158
|
-
def create_entries
|
159
|
-
# ======================================================================= #
|
160
|
-
# === @entry_n_differences
|
161
|
-
#
|
162
|
-
# This is the entry that will simply show the number of differences
|
163
|
-
# between the two sequences, as a number.
|
164
|
-
# ======================================================================= #
|
165
|
-
@entry_n_differences = gtk_entry_with_icon_name('edit-undo-symbolic-rtl.symbolic')
|
166
|
-
@entry_n_differences.xalign = 0.5 # Align towards the center.
|
167
|
-
@entry_n_differences.bblack1
|
168
|
-
@entry_n_differences.clear_background
|
169
|
-
@entry_n_differences.yellow_background
|
170
|
-
|
171
|
-
# ======================================================================= #
|
172
|
-
# === @entry_on_top
|
173
|
-
# ======================================================================= #
|
174
|
-
@entry_on_top = gtk_entry(DEFAULT_TEXT_FOR_ENTRY1)
|
175
|
-
@entry_on_top.set_font(MONOSPACED_FONT)
|
176
|
-
@entry_on_top.clear_background
|
177
|
-
@entry_on_top.css_class('BG_lightsteelblue')
|
178
|
-
@entry_on_top.bblack1
|
179
|
-
@entry_on_top.on_changed { do_calculate_the_differences }
|
180
|
-
@entry_on_top.hint = 'This entry should contain the first sequence (seq1).'
|
181
|
-
@entry_on_top.set_max_length(50_000)
|
182
|
-
@entry_on_top.on_key_press_event { |widget, event|
|
183
|
-
old_text = widget.text
|
184
|
-
keyname = Gdk::Keyval.to_name(event.keyval)
|
185
|
-
case keyname.upcase
|
186
|
-
when *%w( A T C G U )
|
187
|
-
# This is ok.
|
188
|
-
when *%w( B D E F H I J K L M N O P Q R S V W X Y Z ) # Otherwise set the old input here.
|
189
|
-
unless event.state.control_mask? # This snippet checks whether a key-combination has been used.
|
190
|
-
widget.set_text(old_text.upcase)
|
191
|
-
end
|
192
|
-
end
|
193
|
-
} if false # disabled as of August 2022.
|
194
|
-
# ======================================================================= #
|
195
|
-
# And keep things upcased here:
|
196
|
-
# ======================================================================= #
|
197
|
-
@entry_on_top.on_key_release { |widget, event|
|
198
|
-
old_text = @entry_on_top.text
|
199
|
-
new_text = @entry_on_top.text.upcase
|
200
|
-
unless old_text == new_text
|
201
|
-
@entry_on_top.set_text(new_text)
|
202
|
-
@entry_on_top.move_cursor_to_the_most_right_position
|
203
|
-
end
|
204
|
-
}
|
205
|
-
|
206
|
-
# ======================================================================= #
|
207
|
-
# === @entry_on_bottom
|
208
|
-
# ======================================================================= #
|
209
|
-
@entry_on_bottom = gtk_entry(DEFAULT_TEXT_FOR_ENTRY2)
|
210
|
-
@entry_on_bottom.set_font(MONOSPACED_FONT)
|
211
|
-
@entry_on_bottom.css_classes('clear_background BG_lightsteelblue')
|
212
|
-
@entry_on_bottom.bblack1
|
213
|
-
@entry_on_bottom.on_changed { do_calculate_the_differences }
|
214
|
-
@entry_on_bottom.hint = 'This entry should contain the second sequence (seq2).'
|
215
|
-
@entry_on_bottom.set_max_length(50_000)
|
216
|
-
end
|
217
|
-
|
218
|
-
# ========================================================================= #
|
219
|
-
# === create_compare_button
|
220
|
-
#
|
221
|
-
# This method will create the button that will compare the two sequences.
|
222
|
-
# ========================================================================= #
|
223
|
-
def create_compare_button
|
224
|
-
# ======================================================================= #
|
225
|
-
# === @compare_button
|
226
|
-
# ======================================================================= #
|
227
|
-
@compare_button = bold_button(::Bioroebe::GUI::LevenstheinDistanceModule::TEXT_COMPARE_THE_TWO_SEQUENCES)
|
228
|
-
@compare_button.apply_markup
|
229
|
-
@compare_button.lightblue
|
230
|
-
@compare_button.set_name('button1')
|
231
|
-
@compare_button.hint = 'Click this button to '\
|
232
|
-
'<span weight="bold" foreground="lightblue">compare</span> '\
|
233
|
-
'the two sequences.'
|
234
|
-
@compare_button.on_clicked {
|
235
|
-
consider_sanitizing_the_input
|
236
|
-
compare_the_two_sequences
|
237
|
-
}
|
238
|
-
end
|
239
|
-
|
240
|
-
# ========================================================================= #
|
241
|
-
# === create_skeleton (create tag, skeleton tag)
|
242
|
-
# ========================================================================= #
|
243
|
-
def create_skeleton
|
244
|
-
create_entries
|
245
|
-
# ======================================================================= #
|
246
|
-
# === The top box
|
247
|
-
# ======================================================================= #
|
248
|
-
@top_box = vbox
|
249
|
-
|
250
|
-
@label_on_top = bold_label(USE_THIS_TITLE)
|
251
|
-
@label_on_top.hint =
|
252
|
-
"Only <b>valid nucleotides</b> (A, T, C, G, U) \n"\
|
253
|
-
"can be accepted as input."
|
254
|
-
# ======================================================================= #
|
255
|
-
# Create the top hbox for string1 next:
|
256
|
-
# ======================================================================= #
|
257
|
-
@hbox_for_string1 = gtk_hbox
|
258
|
-
@hbox_for_string1.minimal(gtk_label('1').make_bold, 1)
|
259
|
-
@hbox_for_string1.maximal(@entry_on_top, 1)
|
260
|
-
|
261
|
-
# ======================================================================= #
|
262
|
-
# Create the bottom hbox for string2 next:
|
263
|
-
# ======================================================================= #
|
264
|
-
@hbox_for_string2 = gtk_hbox
|
265
|
-
@hbox_for_string2.minimal(gtk_label('2').make_bold, 1)
|
266
|
-
@hbox_for_string2.maximal(@entry_on_bottom, 1)
|
267
|
-
|
268
|
-
create_compare_button
|
269
|
-
|
270
|
-
small_hbox = gtk_hbox
|
271
|
-
# ======================================================================= #
|
272
|
-
# === n_differences found Gtk::Text
|
273
|
-
# ======================================================================= #
|
274
|
-
short_text_widget = gtk_text('<b>n differences</b> found:')
|
275
|
-
short_text_widget.do_markify
|
276
|
-
small_hbox.minimal(short_text_widget, 2)
|
277
|
-
small_hbox.hint =
|
278
|
-
'This entry will show <b>how many differences</b> '\
|
279
|
-
'exist between these two strings.'
|
280
|
-
small_hbox.minimal(@entry_n_differences, 2)
|
281
|
-
# ======================================================================= #
|
282
|
-
# === The bottom box
|
283
|
-
# ======================================================================= #
|
284
|
-
@bottom_box = gtk_vbox
|
285
|
-
@bottom_box.pack_start(@compare_button, expand: false, fill: false, padding: 1)
|
286
|
-
@bottom_box.pack_start(small_hbox, expand: false, fill: true, padding: 0)
|
287
|
-
end
|
288
|
-
|
289
|
-
# ========================================================================= #
|
290
|
-
# === connect_skeleton (connect tag)
|
291
|
-
# ========================================================================= #
|
292
|
-
def connect_skeleton
|
293
|
-
abort_on_exception
|
294
|
-
# ======================================================================= #
|
295
|
-
# @top_box is an instance of gtk-vbox.
|
296
|
-
# ======================================================================= #
|
297
|
-
@top_box.minimal(@label_on_top, 1)
|
298
|
-
text = left_aligned_text(
|
299
|
-
"The <b>Hamming distance</b> - a number - measures the number of "\
|
300
|
-
"\npositions at which two strings of equal length are "\
|
301
|
-
"different.")
|
302
|
-
text.use_this_font = SMALLER_FONT
|
303
|
-
@top_box.minimal(text, 12)
|
304
|
-
@top_box.minimal(@hbox_for_string1, 2)
|
305
|
-
@top_box.minimal(@hbox_for_string2, 2)
|
306
|
-
|
307
|
-
vpaned = mouse_draggable_via_up_and_down_movement(@top_box, @bottom_box)
|
308
|
-
vpaned.set_size_request(@width, 550)
|
309
|
-
maximal(vpaned, 8)
|
310
|
-
show_all
|
311
|
-
end
|
312
|
-
|
313
|
-
# ========================================================================= #
|
314
|
-
# === compare_the_two_sequences
|
315
|
-
#
|
316
|
-
# This is the method that will compare the two sequences.
|
317
|
-
# ========================================================================= #
|
318
|
-
def compare_the_two_sequences
|
319
|
-
do_upcase_all_entries
|
320
|
-
hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
|
321
|
-
@entry_n_differences.set_text(
|
322
|
-
hamming_distance_object.n_differences?.to_s
|
323
|
-
)
|
324
|
-
end; alias do_compare compare_the_two_sequences # === do_compare
|
325
|
-
alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
|
326
|
-
|
327
|
-
# ========================================================================= #
|
328
|
-
# === do_upcase_all_entries
|
329
|
-
# ========================================================================= #
|
330
|
-
def do_upcase_all_entries
|
331
|
-
[
|
332
|
-
@entry_on_top,
|
333
|
-
@entry_on_bottom
|
334
|
-
].each {|entry|
|
335
|
-
entry.do_upcase
|
336
|
-
}
|
337
|
-
end
|
338
|
-
|
339
|
-
# ========================================================================= #
|
340
|
-
# === consider_sanitizing_the_input
|
341
|
-
# ========================================================================= #
|
342
|
-
def consider_sanitizing_the_input
|
343
|
-
# ======================================================================= #
|
344
|
-
# The following two lines were added as of 07.05.2020.
|
345
|
-
# ======================================================================= #
|
346
|
-
@entry_on_top.set_text(@entry_on_top.text.delete('-'))
|
347
|
-
@entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
|
348
|
-
do_upcase_all_entries
|
349
|
-
end
|
350
|
-
|
351
|
-
# ========================================================================= #
|
352
|
-
# === run (run tag)
|
353
|
-
# ========================================================================= #
|
354
|
-
def run
|
355
|
-
create_skeleton_then_connect_skeleton
|
356
|
-
set_minimum_size
|
357
|
-
Thread.new {
|
358
|
-
sleep 0.01
|
359
|
-
@entry_n_differences.do_focus
|
360
|
-
entry1?.deselect
|
361
|
-
do_compare
|
362
|
-
}
|
363
|
-
end
|
364
|
-
|
365
|
-
# ========================================================================= #
|
366
|
-
# === Bioroebe::GUI::Gtk::HammingDistance.run
|
367
|
-
# ========================================================================= #
|
368
|
-
def self.run(
|
369
|
-
i = ARGV
|
370
|
-
)
|
371
|
-
require 'gtk_paradise/run'
|
372
|
-
_ = ::Bioroebe::GUI::Gtk::HammingDistance.new(i)
|
373
|
-
r = ::Gtk.run
|
374
|
-
r << _
|
375
|
-
r.modify_background(:normal, :mintcream)
|
376
|
-
r.automatic_top_left_then_run
|
377
|
-
end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::HammingDistance.run_gtk3_widget
|
378
|
-
|
379
|
-
end; end; end; end
|
380
|
-
|
381
|
-
if __FILE__ == $PROGRAM_NAME
|
382
|
-
Bioroebe::GUI::Gtk::HammingDistance.run
|
383
|
-
end # gtkhammingdistance
|
@@ -1,174 +0,0 @@
|
|
1
|
-
#!/usr/bin/ruby -w
|
2
|
-
# Encoding: UTF-8
|
3
|
-
# frozen_string_literal: true
|
4
|
-
# =========================================================================== #
|
5
|
-
# === Bioroebe::GUI::Gtk::LevenstheinDistance
|
6
|
-
#
|
7
|
-
# This is just a small widget that bundles together a GUI component
|
8
|
-
# towards the Levensthein class.
|
9
|
-
# =========================================================================== #
|
10
|
-
# require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
|
11
|
-
# Bioroebe::GUI::Gtk::LevenstheinDistance.run
|
12
|
-
# =========================================================================== #
|
13
|
-
require 'gtk_paradise/require_gtk3'
|
14
|
-
|
15
|
-
module Bioroebe
|
16
|
-
|
17
|
-
module GUI
|
18
|
-
|
19
|
-
module Gtk
|
20
|
-
|
21
|
-
class LevenstheinDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::LevenstheinDistance
|
22
|
-
|
23
|
-
require 'bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb'
|
24
|
-
include Bioroebe::GUI::LevenstheinDistanceModule
|
25
|
-
|
26
|
-
require 'gtk_paradise/requires/require_the_base_module.rb'
|
27
|
-
include ::Gtk::BaseModule
|
28
|
-
|
29
|
-
# ========================================================================= #
|
30
|
-
# === NAMESPACE
|
31
|
-
# ========================================================================= #
|
32
|
-
NAMESPACE = inspect
|
33
|
-
|
34
|
-
# ========================================================================= #
|
35
|
-
# === initialize
|
36
|
-
# ========================================================================= #
|
37
|
-
def initialize(
|
38
|
-
commandline_arguments = ARGV,
|
39
|
-
run_already = true
|
40
|
-
)
|
41
|
-
super(:vertical)
|
42
|
-
register_sigint
|
43
|
-
reset
|
44
|
-
set_commandline_arguments(
|
45
|
-
commandline_arguments
|
46
|
-
)
|
47
|
-
modify_background(
|
48
|
-
:normal, USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET
|
49
|
-
)
|
50
|
-
run if run_already
|
51
|
-
end
|
52
|
-
|
53
|
-
# ========================================================================= #
|
54
|
-
# === reset (reset tag)
|
55
|
-
# ========================================================================= #
|
56
|
-
def reset
|
57
|
-
reset_the_internal_variables
|
58
|
-
# ======================================================================= #
|
59
|
-
# === @configuration
|
60
|
-
# ======================================================================= #
|
61
|
-
@configuration = [true, __dir__, NAMESPACE]
|
62
|
-
title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
|
63
|
-
use_gtk_paradise_project_CSS_file
|
64
|
-
append_project_CSS_file
|
65
|
-
infer_the_size_automatically
|
66
|
-
instantiate_a_new_levensthein_object
|
67
|
-
end
|
68
|
-
|
69
|
-
# ========================================================================= #
|
70
|
-
# === create_the_grid (grid tag)
|
71
|
-
# ========================================================================= #
|
72
|
-
def create_the_grid
|
73
|
-
# ======================================================================= #
|
74
|
-
# === @grid
|
75
|
-
# ======================================================================= #
|
76
|
-
@grid = gtk_grid
|
77
|
-
@grid.set_column_spacing(4)
|
78
|
-
@grid.set_row_spacing(4)
|
79
|
-
end
|
80
|
-
|
81
|
-
# ========================================================================= #
|
82
|
-
# === populate_the_grid
|
83
|
-
# ========================================================================= #
|
84
|
-
def populate_the_grid
|
85
|
-
@grid.left(@text1)
|
86
|
-
@grid.right(@input_field_for_matches)
|
87
|
-
@grid.new_row
|
88
|
-
@grid.left(@text2)
|
89
|
-
@grid.right(@input_field_for_mismatches)
|
90
|
-
@grid.new_row
|
91
|
-
@grid.left(@text3)
|
92
|
-
@grid.right(@input_field_for_gap_cost)
|
93
|
-
end
|
94
|
-
|
95
|
-
# ========================================================================= #
|
96
|
-
# === connect_skeleton (connect tag)
|
97
|
-
# ========================================================================= #
|
98
|
-
def connect_skeleton
|
99
|
-
abort_on_exception
|
100
|
-
populate_the_grid
|
101
|
-
minimal(@grid, 4)
|
102
|
-
if levensthein_object?.sequence1?
|
103
|
-
unless levensthein_object?.sequence1?.empty?
|
104
|
-
@input_for_string1.set_text(levensthein_object?.sequence1?)
|
105
|
-
end
|
106
|
-
end
|
107
|
-
if levensthein_object?.sequence2?
|
108
|
-
unless levensthein_object?.sequence2?.empty?
|
109
|
-
@input_for_string2.set_text(levensthein_object?.sequence2?)
|
110
|
-
end
|
111
|
-
end
|
112
|
-
minimal(@input_for_string1, 4)
|
113
|
-
minimal(@input_for_string2, 4)
|
114
|
-
# ======================================================================= #
|
115
|
-
# Next below these two input-fields we will add more info:
|
116
|
-
# ======================================================================= #
|
117
|
-
small_label = return_the_edit_distance_label
|
118
|
-
@hbox_with_the_label_for_the_edit_distance = return_hbox_containing_the_edit_distance(
|
119
|
-
small_label, @label_for_the_edit_distance
|
120
|
-
)
|
121
|
-
@hbox4 = return_hbox4(
|
122
|
-
@label_for_the_total_score
|
123
|
-
)
|
124
|
-
minimal(@hbox_with_the_label_for_the_edit_distance, 4)
|
125
|
-
minimal(@hbox4, 4)
|
126
|
-
button_box = gtk_button_box(
|
127
|
-
@button_compare_the_two_strings
|
128
|
-
) { :spread }
|
129
|
-
minimal(button_box, 4)
|
130
|
-
end
|
131
|
-
|
132
|
-
# ========================================================================= #
|
133
|
-
# === create_skeleton (create tag)
|
134
|
-
# ========================================================================= #
|
135
|
-
def create_skeleton
|
136
|
-
create_the_entries
|
137
|
-
create_the_labels
|
138
|
-
create_the_grid
|
139
|
-
create_the_first_row
|
140
|
-
create_the_second_row
|
141
|
-
create_the_third_row
|
142
|
-
create_the_buttons
|
143
|
-
end
|
144
|
-
|
145
|
-
# ========================================================================= #
|
146
|
-
# === run (run tag)
|
147
|
-
# ========================================================================= #
|
148
|
-
def run
|
149
|
-
create_skeleton_then_connect_skeleton
|
150
|
-
show_all
|
151
|
-
check_for_commandline_arguments
|
152
|
-
do_compare_the_two_sequences
|
153
|
-
let_the_fist_entry_respond_to_on_changed_events
|
154
|
-
end
|
155
|
-
|
156
|
-
# ========================================================================= #
|
157
|
-
# === Bioroebe::GUI::Gtk::LevenstheinDistance.run
|
158
|
-
# ========================================================================= #
|
159
|
-
def self.run(
|
160
|
-
i = ARGV
|
161
|
-
)
|
162
|
-
require 'gtk_paradise/run'
|
163
|
-
_ = ::Bioroebe::GUI::Gtk::LevenstheinDistance.new(i)
|
164
|
-
r = ::Gtk.run
|
165
|
-
r << _
|
166
|
-
r.automatic_top_left_then_run
|
167
|
-
end; self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::LevenstheinDistanceModule.start_gui_application
|
168
|
-
self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::LevenstheinDistance.run_gtk3_widget
|
169
|
-
|
170
|
-
end; end; end; end
|
171
|
-
|
172
|
-
if __FILE__ == $PROGRAM_NAME
|
173
|
-
Bioroebe::GUI::Gtk::LevenstheinDistance.run
|
174
|
-
end
|