bioroebe 0.12.24 → 0.13.32
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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 +352 -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 +663 -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 +62 -16
- 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 +15 -15
- 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 +11 -17
- 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 +3 -4
- 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 +17 -16
- 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 +5 -4
- 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 +5607 -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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#!/usr/bin/ruby -w
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# Encoding: UTF-8
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# frozen_string_literal: true
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# =========================================================================== #
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# === Bioroebe::GUI::UniversalWidgets::Alignment
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#
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#
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# =========================================================================== #
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# require 'bioroebe/gui/universal_widgets/alignment/alignment.rb'
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# =========================================================================== #
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require 'universal_widgets/base/base.rb'
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module GUI
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class Alignment < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::Alignment
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include ::Bioroebe::CommandlineArguments
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+
require 'bioroebe/constants/GUIs.rb'
|
29
|
+
require 'bioroebe/toplevel_methods/toplevel_methods.rb'
|
30
|
+
require 'bioroebe/sequence/alignment.rb'
|
31
|
+
|
32
|
+
# ========================================================================= #
|
33
|
+
# === TITLE
|
34
|
+
# ========================================================================= #
|
35
|
+
TITLE = 'Alignment'
|
36
|
+
|
37
|
+
# ========================================================================= #
|
38
|
+
# === WIDTH
|
39
|
+
# ========================================================================= #
|
40
|
+
WIDTH = '65% or 500px minimum'
|
41
|
+
|
42
|
+
# ========================================================================= #
|
43
|
+
# === HEIGHT
|
44
|
+
# ========================================================================= #
|
45
|
+
HEIGHT = '55% or 300px minimum'
|
46
|
+
|
47
|
+
# ========================================================================= #
|
48
|
+
# === USE_THIS_FONT
|
49
|
+
# ========================================================================= #
|
50
|
+
USE_THIS_FONT = :hack_26
|
51
|
+
|
52
|
+
# ========================================================================= #
|
53
|
+
# === FONT_FOR_THE_ENTRIES
|
54
|
+
#
|
55
|
+
# The entries must use a mono-spaced font.
|
56
|
+
# ========================================================================= #
|
57
|
+
FONT_FOR_THE_ENTRIES = :hack_22
|
58
|
+
|
59
|
+
# ========================================================================= #
|
60
|
+
# === TEXT_INPUT_THE_SEQUENCES
|
61
|
+
# ========================================================================= #
|
62
|
+
TEXT_INPUT_THE_SEQUENCES = 'Input the sequences that you wish '\
|
63
|
+
'to compare to one another'
|
64
|
+
|
65
|
+
# ========================================================================= #
|
66
|
+
# === TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
|
67
|
+
# ========================================================================= #
|
68
|
+
TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON =
|
69
|
+
"Click on this button to analyse the given sequence. Make sure "\
|
70
|
+
"to use <b>newlines</b> in order to split the sequence at hand."
|
71
|
+
|
72
|
+
# ========================================================================= #
|
73
|
+
# === TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE
|
74
|
+
#
|
75
|
+
# This is the base-tooltip for the entry that retains our consensus
|
76
|
+
# sequence.
|
77
|
+
# ========================================================================= #
|
78
|
+
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE =
|
79
|
+
'This entry will contain the <b>consensus sequence</b>, '\
|
80
|
+
'derived from the above sequences.'
|
81
|
+
|
82
|
+
# ========================================================================= #
|
83
|
+
# === TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
|
84
|
+
# ========================================================================= #
|
85
|
+
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION =
|
86
|
+
"\n\nTake note that in the event that there is <b>an even number of "\
|
87
|
+
"input sequences</b>, the entries defined before will take precedence. "\
|
88
|
+
"So, for instance, if you have four sequences in total, where two are "\
|
89
|
+
"ATTA and the next two are ATTT, then the consensus sequence is "\
|
90
|
+
"currently assumed to be <b>ATTA</b>."
|
91
|
+
|
92
|
+
# ========================================================================= #
|
93
|
+
# === initialize
|
94
|
+
# ========================================================================= #
|
95
|
+
def initialize(
|
96
|
+
commandline_arguments = nil,
|
97
|
+
run_already = true
|
98
|
+
)
|
99
|
+
determine_the_GUI_to_be_used(commandline_arguments)
|
100
|
+
reset
|
101
|
+
set_commandline_arguments(
|
102
|
+
commandline_arguments
|
103
|
+
)
|
104
|
+
run if run_already
|
105
|
+
end
|
106
|
+
|
107
|
+
# ========================================================================= #
|
108
|
+
# === reset (reset tag)
|
109
|
+
# ========================================================================= #
|
110
|
+
def reset
|
111
|
+
super() if respond_to?(:super)
|
112
|
+
reset_the_internal_variables
|
113
|
+
reset_the_base_module # This must come after reset_the_internal_variables().
|
114
|
+
infer_the_namespace
|
115
|
+
# ======================================================================= #
|
116
|
+
# === @configuration
|
117
|
+
# ======================================================================= #
|
118
|
+
@configuration = [true, __dir__, namespace?]
|
119
|
+
# ======================================================================= #
|
120
|
+
# === Set the title, width, height and the font in use.
|
121
|
+
# ======================================================================= #
|
122
|
+
title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
|
123
|
+
handle_CSS if use_gtk3?
|
124
|
+
reset_the_alignment_object
|
125
|
+
end
|
126
|
+
|
127
|
+
# ========================================================================= #
|
128
|
+
# === handle_CSS_rules (CSS tag)
|
129
|
+
# ========================================================================= #
|
130
|
+
def handle_CSS_rules
|
131
|
+
use_gtk_paradise_project_css_file
|
132
|
+
append_project_css_file
|
133
|
+
apply_the_CSS_rules
|
134
|
+
end; alias handle_CSS handle_CSS_rules # === handle_CSS
|
135
|
+
|
136
|
+
# ========================================================================= #
|
137
|
+
# === return_the_first_row
|
138
|
+
# ========================================================================= #
|
139
|
+
def return_the_first_row
|
140
|
+
_ = create_hbox
|
141
|
+
top_label = left_aligned_label(
|
142
|
+
TEXT_INPUT_THE_SEQUENCES
|
143
|
+
)
|
144
|
+
top_label.make_selectable
|
145
|
+
top_label.center
|
146
|
+
_.minimal(top_label)
|
147
|
+
use_this_image = image_document_open
|
148
|
+
if use_this_image
|
149
|
+
event_box = event_box(use_this_image)
|
150
|
+
if event_box
|
151
|
+
event_box.hint = 'Click on this icon to open a local file.'
|
152
|
+
event_box.on_clicked {
|
153
|
+
do_open_and_assign_a_local_file
|
154
|
+
}
|
155
|
+
_.pack_end(event_box)
|
156
|
+
end
|
157
|
+
end
|
158
|
+
return _
|
159
|
+
end
|
160
|
+
|
161
|
+
# ========================================================================= #
|
162
|
+
# === create_the_entries (entry tag, entries tag)
|
163
|
+
# ========================================================================= #
|
164
|
+
def create_the_entries
|
165
|
+
create_the_consensus_sequence_entry
|
166
|
+
# ======================================================================= #
|
167
|
+
# === @entry_numbers
|
168
|
+
# ======================================================================= #
|
169
|
+
@entry_numbers = create_entry
|
170
|
+
@entry_numbers.bblack1
|
171
|
+
@entry_numbers.use_this_font = FONT_FOR_THE_ENTRIES
|
172
|
+
@entry_numbers.hint =
|
173
|
+
'This area may indicate the numbers for '\
|
174
|
+
'the alignment shown right above.'
|
175
|
+
@entry_numbers.very_light_yellow_background
|
176
|
+
end
|
177
|
+
|
178
|
+
# ========================================================================= #
|
179
|
+
# === create_the_text_buffer_and_the_text_view
|
180
|
+
# ========================================================================= #
|
181
|
+
def create_the_text_buffer_and_the_text_view
|
182
|
+
# ======================================================================= #
|
183
|
+
# === @text_buffer
|
184
|
+
# ======================================================================= #
|
185
|
+
@text_buffer = create_text_buffer
|
186
|
+
# ======================================================================= #
|
187
|
+
# === @text_view
|
188
|
+
# ======================================================================= #
|
189
|
+
@text_view = create_text_view(@text_buffer)
|
190
|
+
end
|
191
|
+
|
192
|
+
# ========================================================================= #
|
193
|
+
# === textview?
|
194
|
+
# ========================================================================= #
|
195
|
+
def textview?
|
196
|
+
@text_view
|
197
|
+
end
|
198
|
+
|
199
|
+
# ========================================================================= #
|
200
|
+
# === create_the_scrolled_window
|
201
|
+
# ========================================================================= #
|
202
|
+
def create_the_scrolled_window
|
203
|
+
# ======================================================================= #
|
204
|
+
# === @scrolled_window
|
205
|
+
# ======================================================================= #
|
206
|
+
@scrolled_window = create_scrolled_window(@text_view)
|
207
|
+
@scrolled_window.width_height(300, 400)
|
208
|
+
@scrolled_window.pad4px
|
209
|
+
@scrolled_window.bblack2
|
210
|
+
end
|
211
|
+
|
212
|
+
# ========================================================================= #
|
213
|
+
# === padding?
|
214
|
+
# ========================================================================= #
|
215
|
+
def padding?
|
216
|
+
12
|
217
|
+
end
|
218
|
+
|
219
|
+
# ========================================================================= #
|
220
|
+
# === border_size?
|
221
|
+
# ========================================================================= #
|
222
|
+
def border_size?
|
223
|
+
8
|
224
|
+
end
|
225
|
+
|
226
|
+
# ========================================================================= #
|
227
|
+
# === smaller_font?
|
228
|
+
# ========================================================================= #
|
229
|
+
def smaller_font?
|
230
|
+
SMALLER_FONT
|
231
|
+
end
|
232
|
+
|
233
|
+
# ========================================================================= #
|
234
|
+
# === the_do_analyse_button_was_clicked
|
235
|
+
# ========================================================================= #
|
236
|
+
def the_do_analyse_button_was_clicked
|
237
|
+
do_analyse
|
238
|
+
realign_the_numbers_showing_how_long_the_consensus_sequence_is
|
239
|
+
update_the_hint_for_the_entry_consequences_sequence(
|
240
|
+
(
|
241
|
+
"This entry will contain the consensus sequence, "\
|
242
|
+
"derived from the above "+
|
243
|
+
(@text_buffer.text?.count("\n")+1).to_s+" sequences.\n\nNote "\
|
244
|
+
"that only the minimal length will be compared - "\
|
245
|
+
"superfluous nucleotides will NOT be considered unless "\
|
246
|
+
"they can be aligned to other sequences."+
|
247
|
+
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
|
248
|
+
).squeeze(' ')
|
249
|
+
)
|
250
|
+
end
|
251
|
+
|
252
|
+
# ========================================================================= #
|
253
|
+
# === create_the_skeleton (create tag, skeleton tag)
|
254
|
+
# ========================================================================= #
|
255
|
+
def create_the_skeleton
|
256
|
+
create_the_checkboxes # Create the checkboxes first.
|
257
|
+
create_the_entries
|
258
|
+
create_the_buttons
|
259
|
+
create_the_text_buffer_and_the_text_view
|
260
|
+
create_the_scrolled_window
|
261
|
+
end
|
262
|
+
|
263
|
+
# ========================================================================= #
|
264
|
+
# === create_the_checkboxes
|
265
|
+
# ========================================================================= #
|
266
|
+
def create_the_checkboxes
|
267
|
+
# ======================================================================= #
|
268
|
+
# === @checkbox1
|
269
|
+
# ======================================================================= #
|
270
|
+
@checkbox1 = create_checkbox
|
271
|
+
@checkbox1.is_active
|
272
|
+
@checkbox2 = create_checkbox
|
273
|
+
end
|
274
|
+
|
275
|
+
# ========================================================================= #
|
276
|
+
# === button_convert?
|
277
|
+
# ========================================================================= #
|
278
|
+
def button_convert?
|
279
|
+
@button_convert
|
280
|
+
end
|
281
|
+
|
282
|
+
|
283
|
+
# ========================================================================= #
|
284
|
+
# === create_the_buttons (buttons tag)
|
285
|
+
# ========================================================================= #
|
286
|
+
def create_the_buttons
|
287
|
+
# ======================================================================= #
|
288
|
+
# === @button_do_analyse
|
289
|
+
# ======================================================================= #
|
290
|
+
@button_do_analyse = bold_button('_Do analyse', self, :use_mnemonic) {
|
291
|
+
:the_do_analyse_button_was_clicked
|
292
|
+
}
|
293
|
+
@button_do_analyse.clear_background
|
294
|
+
@button_do_analyse.bblack1
|
295
|
+
@button_do_analyse.on_hover(:lightblue)
|
296
|
+
@button_do_analyse.hint = TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
|
297
|
+
end
|
298
|
+
|
299
|
+
# ========================================================================= #
|
300
|
+
# === do_trigger_the_conversion (conversion tag)
|
301
|
+
#
|
302
|
+
# This method is the one that will convert from the three-letter to the
|
303
|
+
# one-letter and vice versa.
|
304
|
+
# ========================================================================= #
|
305
|
+
def do_trigger_the_conversion(
|
306
|
+
i = @entry1.text?,
|
307
|
+
checkbox1 = @checkbox1
|
308
|
+
)
|
309
|
+
i = i.to_s.dup.delete(' ')
|
310
|
+
if checkbox1.active?
|
311
|
+
new_result = Bioroebe.three_to_one(i).to_s
|
312
|
+
else
|
313
|
+
new_result = Bioroebe.one_to_three(i).to_s
|
314
|
+
end
|
315
|
+
if new_result and !new_result.empty?
|
316
|
+
@entry2.set_text(new_result)
|
317
|
+
@entry2.make_bold
|
318
|
+
end
|
319
|
+
end; alias do_the_conversion do_trigger_the_conversion # === do_the_conversion
|
320
|
+
|
321
|
+
# ========================================================================= #
|
322
|
+
# === return_the_checkbox_widget
|
323
|
+
# ========================================================================= #
|
324
|
+
def return_the_checkbox_widget
|
325
|
+
smaller_font = smaller_font?
|
326
|
+
grid = default_grid
|
327
|
+
text1 = text('3-to-1 conversion')
|
328
|
+
text1.use_this_font(smaller_font)
|
329
|
+
text1.hint = 'Convert the three letter code to the one letter code.'
|
330
|
+
pp text1
|
331
|
+
grid.left(text1)
|
332
|
+
grid.right(@checkbox1)
|
333
|
+
text2 = text('1-to-3 conversion')
|
334
|
+
text2.use_this_font(smaller_font)
|
335
|
+
text2.hint = 'Convert the one letter code to the three letter code.'
|
336
|
+
grid.left(text2)
|
337
|
+
grid.right(@checkbox2)
|
338
|
+
@checkbox1.on_toggled {
|
339
|
+
if @checkbox1.active? == false
|
340
|
+
@checkbox2.is_now_active
|
341
|
+
else
|
342
|
+
@checkbox2.is_now_inactive
|
343
|
+
end
|
344
|
+
}
|
345
|
+
@checkbox2.on_toggled {
|
346
|
+
if @checkbox2.active? == false
|
347
|
+
@checkbox1.is_now_active
|
348
|
+
else
|
349
|
+
@checkbox1.is_now_inactive
|
350
|
+
end
|
351
|
+
}
|
352
|
+
return grid
|
353
|
+
end
|
354
|
+
|
355
|
+
# ========================================================================= #
|
356
|
+
# === do_analyse
|
357
|
+
#
|
358
|
+
# This method will be called whenever the user hits the "Do analyse"
|
359
|
+
# button.
|
360
|
+
# ========================================================================= #
|
361
|
+
def do_analyse(
|
362
|
+
_ = text_buffer?.text?
|
363
|
+
)
|
364
|
+
if _ and !_.empty?
|
365
|
+
_.strip!
|
366
|
+
alignment?.use_this_as_input(_)
|
367
|
+
consensus_sequence = return_the_consensus_sequence
|
368
|
+
@entry_consensus_sequence.set_text(consensus_sequence)
|
369
|
+
else
|
370
|
+
pop_up_widget(
|
371
|
+
over_this_widget: text_view_widget?,
|
372
|
+
text: 'Please assign a sequence first.'
|
373
|
+
)
|
374
|
+
end
|
375
|
+
end; alias do_analyse_again do_analyse # === do_analyse_again
|
376
|
+
|
377
|
+
# ========================================================================= #
|
378
|
+
# === run (run tag)
|
379
|
+
# ========================================================================= #
|
380
|
+
def run
|
381
|
+
run_super
|
382
|
+
end
|
383
|
+
|
384
|
+
# ========================================================================= #
|
385
|
+
# === return_the_consensus_sequence
|
386
|
+
# ========================================================================= #
|
387
|
+
def return_the_consensus_sequence
|
388
|
+
@alignment.consensus_sequence?
|
389
|
+
end
|
390
|
+
|
391
|
+
# ========================================================================= #
|
392
|
+
# === text_view_widget?
|
393
|
+
# ========================================================================= #
|
394
|
+
def text_view_widget?
|
395
|
+
@text_view
|
396
|
+
end
|
397
|
+
|
398
|
+
# ========================================================================= #
|
399
|
+
# === realign_the_numbers_showing_how_long_the_consensus_sequence_is
|
400
|
+
# ========================================================================= #
|
401
|
+
def realign_the_numbers_showing_how_long_the_consensus_sequence_is
|
402
|
+
@entry_numbers.center if @entry_numbers.respond_to?(:center)
|
403
|
+
n_characters = @entry_consensus_sequence.text?.size
|
404
|
+
@entry_numbers.set_text(return_fill_up_to(n_characters))
|
405
|
+
end
|
406
|
+
|
407
|
+
# ========================================================================= #
|
408
|
+
# === create_the_consensus_sequence_entry
|
409
|
+
# ========================================================================= #
|
410
|
+
def create_the_consensus_sequence_entry
|
411
|
+
# ======================================================================= #
|
412
|
+
# === @entry_consensus_sequence
|
413
|
+
# ======================================================================= #
|
414
|
+
@entry_consensus_sequence = entry
|
415
|
+
@entry_consensus_sequence.bblack1
|
416
|
+
@entry_consensus_sequence.center
|
417
|
+
@entry_consensus_sequence.use_this_font = FONT_FOR_THE_ENTRIES
|
418
|
+
@entry_consensus_sequence.yellow_background
|
419
|
+
update_the_hint_for_the_entry_consequences_sequence(
|
420
|
+
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE+
|
421
|
+
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
|
422
|
+
)
|
423
|
+
end
|
424
|
+
|
425
|
+
# ========================================================================= #
|
426
|
+
# === entry_consensus_sequence?
|
427
|
+
# ========================================================================= #
|
428
|
+
def entry_consensus_sequence?
|
429
|
+
@entry_consensus_sequence
|
430
|
+
end
|
431
|
+
|
432
|
+
# ========================================================================= #
|
433
|
+
# === return_fill_up_to
|
434
|
+
# ========================================================================= #
|
435
|
+
def return_fill_up_to(i)
|
436
|
+
_ = ''.dup
|
437
|
+
i.times {|counter|
|
438
|
+
counter = (counter+1) % 10
|
439
|
+
_ << counter.to_s
|
440
|
+
}
|
441
|
+
return _
|
442
|
+
end
|
443
|
+
|
444
|
+
# ========================================================================= #
|
445
|
+
# === do_open_and_assign_a_local_file
|
446
|
+
# ========================================================================= #
|
447
|
+
def do_open_and_assign_a_local_file
|
448
|
+
open_local_file {{
|
449
|
+
start_directory: log_dir?,
|
450
|
+
additional_folders: [
|
451
|
+
log_dir?,
|
452
|
+
'/Depot/j/',
|
453
|
+
'/Depot/jj/',
|
454
|
+
'/Depot/jjj/',
|
455
|
+
'/Depot/jjjj/'
|
456
|
+
]
|
457
|
+
}}
|
458
|
+
_ = main_file?
|
459
|
+
if _ and File.exist?(_)
|
460
|
+
dataset = File.read(_)
|
461
|
+
@text_buffer.set_text(dataset)
|
462
|
+
do_analyse_again
|
463
|
+
end
|
464
|
+
end
|
465
|
+
|
466
|
+
# ========================================================================= #
|
467
|
+
# === update_the_hint_for_the_entry_consequences_sequence
|
468
|
+
# ========================================================================= #
|
469
|
+
def update_the_hint_for_the_entry_consequences_sequence(
|
470
|
+
i = ''
|
471
|
+
)
|
472
|
+
@entry_consensus_sequence.hint = i
|
473
|
+
end
|
474
|
+
|
475
|
+
# ========================================================================= #
|
476
|
+
# === alignment?
|
477
|
+
# ========================================================================= #
|
478
|
+
def alignment?
|
479
|
+
@alignment
|
480
|
+
end
|
481
|
+
|
482
|
+
# ========================================================================= #
|
483
|
+
# === text_buffer?
|
484
|
+
# ========================================================================= #
|
485
|
+
def text_buffer?
|
486
|
+
@text_buffer
|
487
|
+
end
|
488
|
+
|
489
|
+
# ========================================================================= #
|
490
|
+
# === reset_the_alignment_object
|
491
|
+
# ========================================================================= #
|
492
|
+
def reset_the_alignment_object
|
493
|
+
# ======================================================================= #
|
494
|
+
# === @alignment
|
495
|
+
# ======================================================================= #
|
496
|
+
@alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
|
497
|
+
end
|
498
|
+
|
499
|
+
# ========================================================================= #
|
500
|
+
# === Bioroebe::GUI::UniversalWidgets::Alignment[]
|
501
|
+
# ========================================================================= #
|
502
|
+
def self.[](i = ARGV)
|
503
|
+
new(i)
|
504
|
+
end
|
505
|
+
|
506
|
+
# ========================================================================= #
|
507
|
+
# === Bioroebe::GUI::Gtk::Alignment.run
|
508
|
+
# ========================================================================= #
|
509
|
+
def self.run(
|
510
|
+
i = ARGV
|
511
|
+
)
|
512
|
+
::Gtk.gtk_runner_factory(
|
513
|
+
::Bioroebe::GUI::Gtk::Alignment.new(i)
|
514
|
+
)
|
515
|
+
end
|
516
|
+
|
517
|
+
# ========================================================================= #
|
518
|
+
# === connect_the_skeleton (connect tag, skeleton tag)
|
519
|
+
# ========================================================================= #
|
520
|
+
def connect_the_skeleton
|
521
|
+
abort_on_exception
|
522
|
+
|
523
|
+
grid = default_grid
|
524
|
+
grid.full_row(return_the_first_row)
|
525
|
+
grid.full_row(@scrolled_window)
|
526
|
+
grid.full_row(@entry_consensus_sequence)
|
527
|
+
grid.full_row(@entry_numbers)
|
528
|
+
grid.full_row(@button_do_analyse)
|
529
|
+
grid.hcenter
|
530
|
+
|
531
|
+
window = runner_widget(nil, width?, height?, title?)
|
532
|
+
window << grid
|
533
|
+
do_focus_on_the_textview
|
534
|
+
::UniversalWidgets.set_main_window(window)
|
535
|
+
upon_delete_event_quit_the_application
|
536
|
+
window.use_this_font = font?
|
537
|
+
window.show_all
|
538
|
+
window.set_size_request(width?, height?)
|
539
|
+
window.set_default_size(width?, height?)
|
540
|
+
window.set_padding(padding?)
|
541
|
+
window.set_border_size(border_size?)
|
542
|
+
window.top_left
|
543
|
+
run_main
|
544
|
+
end
|
545
|
+
|
546
|
+
# ========================================================================= #
|
547
|
+
# === do_focus_on_the_textview
|
548
|
+
# ========================================================================= #
|
549
|
+
def do_focus_on_the_textview
|
550
|
+
textview?.do_focus
|
551
|
+
end
|
552
|
+
|
553
|
+
end; end; end; end
|
554
|
+
|
555
|
+
if __FILE__ == $PROGRAM_NAME
|
556
|
+
Bioroebe::GUI::UniversalWidgets::Alignment.new(ARGV)
|
557
|
+
end # gui_alignment
|