bioroebe 0.10.80
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- checksums.yaml +7 -0
- data/LICENSE.md +428 -0
- data/README.md +9280 -0
- data/bin/advanced_dotplot +7 -0
- data/bin/align_open_reading_frames +12 -0
- data/bin/all_positions_of_this_nucleotide +7 -0
- data/bin/aminoacid_composition +7 -0
- data/bin/aminoacid_frequencies +12 -0
- data/bin/aminoacid_substitution +7 -0
- data/bin/automatically_rename_this_fasta_file +7 -0
- data/bin/base_composition +7 -0
- data/bin/batch_create_windows_executables +7 -0
- data/bin/biomart_console +11 -0
- data/bin/bioroebe +27 -0
- data/bin/bioroebe_controller +10 -0
- data/bin/bioshell +26 -0
- data/bin/blosum_2D_table +12 -0
- data/bin/calculate_n50_value +12 -0
- data/bin/chunked_display +12 -0
- data/bin/codon_frequency +9 -0
- data/bin/codon_to_aminoacid +30 -0
- data/bin/colourize_this_fasta_sequence +14 -0
- data/bin/compact_fasta_file +7 -0
- data/bin/complement +7 -0
- data/bin/complementary_dna_strand +12 -0
- data/bin/complementary_rna_strand +12 -0
- data/bin/compseq +7 -0
- data/bin/consensus_sequence +17 -0
- data/bin/count_AT +12 -0
- data/bin/count_GC +12 -0
- data/bin/create_random_aminoacids +7 -0
- data/bin/decode_this_aminoacid_sequence +20 -0
- data/bin/deduce_aminoacid_sequence +13 -0
- data/bin/deduce_most_likely_aminoacid_sequence +7 -0
- data/bin/display_aminoacid_table +12 -0
- data/bin/display_open_reading_frames +7 -0
- data/bin/dna_to_aminoacid_sequence +7 -0
- data/bin/dna_to_rna +7 -0
- data/bin/downcase_chunked_display +12 -0
- data/bin/download_this_pdb +7 -0
- data/bin/fasta_index +7 -0
- data/bin/fetch_data_from_uniprot +12 -0
- data/bin/filter_away_invalid_nucleotides +12 -0
- data/bin/find_substring +19 -0
- data/bin/genbank_to_fasta +7 -0
- data/bin/hamming_distance +12 -0
- data/bin/input_as_dna +12 -0
- data/bin/is_palindrome +13 -0
- data/bin/leading_five_prime +7 -0
- data/bin/levensthein +7 -0
- data/bin/longest_ORF +14 -0
- data/bin/longest_substring +12 -0
- data/bin/n_stop_codons_in_this_sequence +15 -0
- data/bin/open_reading_frames +14 -0
- data/bin/overwrite_fasta_header +7 -0
- data/bin/palindrome_2D_structure +7 -0
- data/bin/palindrome_generator +7 -0
- data/bin/parse_fasta +7 -0
- data/bin/partner_nucleotide +9 -0
- data/bin/possible_codons_for_this_aminoacid +12 -0
- data/bin/random_dna_sequence +12 -0
- data/bin/random_sequence +12 -0
- data/bin/raw_hamming_distance +12 -0
- data/bin/return_longest_substring_via_LCS_algorithm +7 -0
- data/bin/reverse_complement +7 -0
- data/bin/reverse_sequence +7 -0
- data/bin/ruler +12 -0
- data/bin/scan_this_input_for_startcodons +12 -0
- data/bin/short_aminoacid_letter_from_long_aminoacid_name +7 -0
- data/bin/show_atomic_composition +7 -0
- data/bin/show_codon_usage +12 -0
- data/bin/show_fasta_header +7 -0
- data/bin/show_nucleotide_sequence +7 -0
- data/bin/show_this_codon_table +7 -0
- data/bin/show_this_dna_sequence +7 -0
- data/bin/showorf +14 -0
- data/bin/simplify_fasta +7 -0
- data/bin/sort_aminoacid_based_on_its_hydrophobicity +7 -0
- data/bin/split_this_fasta_file_into_chromosomes +7 -0
- data/bin/strict_filter_away_invalid_aminoacids +7 -0
- data/bin/taxonomy +63 -0
- data/bin/three_to_one +7 -0
- data/bin/to_rna +7 -0
- data/bin/trailing_three_prime +7 -0
- data/bin/trypsin_digest +7 -0
- data/bin/upcase_this_aminoacid_sequence_and_remove_numbers +7 -0
- data/bioroebe.gemspec +97 -0
- data/doc/IUPAC_aminoacids_code.md +36 -0
- data/doc/IUPAC_nucleotide_code.md +19 -0
- data/doc/README.gen +9237 -0
- data/doc/blosum.md +5 -0
- data/doc/compatibility/BIO_PHP.md +37 -0
- data/doc/compatibility/README.md +3 -0
- data/doc/compatibility/emboss.md +56 -0
- data/doc/extensive_usage_example.md +35 -0
- data/doc/german_names_for_the_aminoacids.md +27 -0
- data/doc/instructions_for_the_taxonomy_subproject.md +504 -0
- data/doc/legacy_paths.md +9 -0
- data/doc/pdb_ATOM_entry.md +33 -0
- data/doc/quality_control/README.md +2 -0
- data/doc/quality_control/commandline_applications.md +13 -0
- data/doc/resources.md +23 -0
- data/doc/setup.rb +1655 -0
- data/doc/statistics/statistics.md +41 -0
- data/doc/todo/README.md +5 -0
- data/doc/todo/bioroebe_GUI_todo.md +15 -0
- data/doc/todo/bioroebe_todo.md +2823 -0
- data/doc/using_biomart.md +258 -0
- data/html/test.html +144 -0
- data/lib/bioroebe/aminoacids/aminoacid_substitution.rb +118 -0
- data/lib/bioroebe/aminoacids/aminoacids_mass_table.rb +118 -0
- data/lib/bioroebe/aminoacids/codon_percentage.rb +189 -0
- data/lib/bioroebe/aminoacids/colourize_hydrophilic_and_hydrophobic_aminoacids.rb +110 -0
- data/lib/bioroebe/aminoacids/create_random_aminoacids.rb +221 -0
- data/lib/bioroebe/aminoacids/deduce_aminoacid_sequence.rb +460 -0
- data/lib/bioroebe/aminoacids/display_aminoacid_table.rb +231 -0
- data/lib/bioroebe/aminoacids/show_hydrophobicity.rb +184 -0
- data/lib/bioroebe/annotations/README.md +2 -0
- data/lib/bioroebe/annotations/create_annotation_format.rb +208 -0
- data/lib/bioroebe/autoinclude.rb +7 -0
- data/lib/bioroebe/base/base.rb +35 -0
- data/lib/bioroebe/base/colours.rb +14 -0
- data/lib/bioroebe/base/colours_for_base/colours_for_base.rb +275 -0
- data/lib/bioroebe/base/commandline_application/README.md +7 -0
- data/lib/bioroebe/base/commandline_application/aminoacids.rb +33 -0
- data/lib/bioroebe/base/commandline_application/commandline_application.rb +37 -0
- data/lib/bioroebe/base/commandline_application/commandline_arguments.rb +144 -0
- data/lib/bioroebe/base/commandline_application/directory.rb +33 -0
- data/lib/bioroebe/base/commandline_application/extract.rb +22 -0
- data/lib/bioroebe/base/commandline_application/misc.rb +485 -0
- data/lib/bioroebe/base/commandline_application/opn.rb +47 -0
- data/lib/bioroebe/base/commandline_application/reset.rb +40 -0
- data/lib/bioroebe/base/commandline_application/warnings.rb +36 -0
- data/lib/bioroebe/base/commandline_application/write_what_into.rb +29 -0
- data/lib/bioroebe/base/initialize.rb +18 -0
- data/lib/bioroebe/base/misc.rb +94 -0
- data/lib/bioroebe/base/namespace.rb +16 -0
- data/lib/bioroebe/base/prototype/README.md +12 -0
- data/lib/bioroebe/base/prototype/e_and_ee.rb +24 -0
- data/lib/bioroebe/base/prototype/misc.rb +108 -0
- data/lib/bioroebe/base/prototype/mkdir.rb +20 -0
- data/lib/bioroebe/base/prototype/prototype.rb +21 -0
- data/lib/bioroebe/base/prototype/reset.rb +26 -0
- data/lib/bioroebe/base/reset.rb +11 -0
- data/lib/bioroebe/biomart/LICENSE.md +27 -0
- data/lib/bioroebe/biomart/attribute.rb +77 -0
- data/lib/bioroebe/biomart/biomart.rb +227 -0
- data/lib/bioroebe/biomart/database.rb +128 -0
- data/lib/bioroebe/biomart/dataset.rb +572 -0
- data/lib/bioroebe/biomart/filter.rb +97 -0
- data/lib/bioroebe/biomart/server.rb +152 -0
- data/lib/bioroebe/blosum/blosum.rb +88 -0
- data/lib/bioroebe/calculate/calculate_blosum_score.rb +145 -0
- data/lib/bioroebe/calculate/calculate_gc_content.rb +301 -0
- data/lib/bioroebe/calculate/calculate_levensthein_distance.rb +100 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature.rb +398 -0
- data/lib/bioroebe/calculate/calculate_melting_temperature_for_more_than_thirteen_nucleotides.rb +304 -0
- data/lib/bioroebe/calculate/calculate_the_position_specific_scoring_matrix.rb +166 -0
- data/lib/bioroebe/cell/README.md +1 -0
- data/lib/bioroebe/cell/cell.rb +63 -0
- data/lib/bioroebe/cleave_and_digest/README.md +2 -0
- data/lib/bioroebe/cleave_and_digest/cleave.rb +80 -0
- data/lib/bioroebe/cleave_and_digest/digestion.rb +75 -0
- data/lib/bioroebe/cleave_and_digest/trypsin.rb +192 -0
- data/lib/bioroebe/codon_tables/README.md +9 -0
- data/lib/bioroebe/codon_tables/frequencies/287_Pseudomonas_aeruginosa.yml +101 -0
- data/lib/bioroebe/codon_tables/frequencies/3702_Arabidopsis_thaliana.yml +77 -0
- data/lib/bioroebe/codon_tables/frequencies/4932_Saccharomyces_cerevisiae.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/7227_Drosophila_melanogaster.yml +71 -0
- data/lib/bioroebe/codon_tables/frequencies/83333_Escherichia_coli_K12.yml +103 -0
- data/lib/bioroebe/codon_tables/frequencies/9606_Homo_sapiens.yml +123 -0
- data/lib/bioroebe/codon_tables/frequencies/9685_Felis_catus.yml +78 -0
- data/lib/bioroebe/codon_tables/frequencies/README.md +10 -0
- data/lib/bioroebe/codon_tables/frequencies/parse_frequency_table.rb +337 -0
- data/lib/bioroebe/codons/README.md +28 -0
- data/lib/bioroebe/codons/codon_table.rb +416 -0
- data/lib/bioroebe/codons/codon_tables.rb +123 -0
- data/lib/bioroebe/codons/codons.rb +517 -0
- data/lib/bioroebe/codons/convert_this_codon_to_that_aminoacid.rb +102 -0
- data/lib/bioroebe/codons/detect_minimal_codon.rb +180 -0
- data/lib/bioroebe/codons/determine_optimal_codons.rb +74 -0
- data/lib/bioroebe/codons/possible_codons_for_this_aminoacid.rb +380 -0
- data/lib/bioroebe/codons/sanitize_codon_frequency.rb +144 -0
- data/lib/bioroebe/codons/show_codon_tables.rb +130 -0
- data/lib/bioroebe/codons/show_codon_usage.rb +197 -0
- data/lib/bioroebe/codons/show_this_codon_table.rb +573 -0
- data/lib/bioroebe/codons/start_codons.rb +105 -0
- data/lib/bioroebe/colours/colour_schemes/README.md +10 -0
- data/lib/bioroebe/colours/colour_schemes/array_available_colour_schemes.rb +38 -0
- data/lib/bioroebe/colours/colour_schemes/buried.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme.rb +101 -0
- data/lib/bioroebe/colours/colour_schemes/colour_scheme_demo.rb +262 -0
- data/lib/bioroebe/colours/colour_schemes/helix.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/hydropathy.rb +70 -0
- data/lib/bioroebe/colours/colour_schemes/nucleotide.rb +47 -0
- data/lib/bioroebe/colours/colour_schemes/score.rb +112 -0
- data/lib/bioroebe/colours/colour_schemes/simple.rb +42 -0
- data/lib/bioroebe/colours/colour_schemes/strand.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/taylor.rb +58 -0
- data/lib/bioroebe/colours/colour_schemes/turn.rb +65 -0
- data/lib/bioroebe/colours/colour_schemes/zappo.rb +59 -0
- data/lib/bioroebe/colours/colourize_sequence.rb +262 -0
- data/lib/bioroebe/colours/colours.rb +119 -0
- data/lib/bioroebe/colours/misc_colours.rb +80 -0
- data/lib/bioroebe/colours/rev.rb +41 -0
- data/lib/bioroebe/colours/sdir.rb +21 -0
- data/lib/bioroebe/colours/sfancy.rb +21 -0
- data/lib/bioroebe/colours/sfile.rb +21 -0
- data/lib/bioroebe/colours/simp.rb +21 -0
- data/lib/bioroebe/colours/swarn.rb +29 -0
- data/lib/bioroebe/colours/use_colours.rb +27 -0
- data/lib/bioroebe/configuration/configuration.rb +114 -0
- data/lib/bioroebe/configuration/constants.rb +35 -0
- data/lib/bioroebe/constants/GUIs.rb +79 -0
- data/lib/bioroebe/constants/aminoacids_and_proteins.rb +146 -0
- data/lib/bioroebe/constants/base_directory.rb +120 -0
- data/lib/bioroebe/constants/carriage_return.rb +14 -0
- data/lib/bioroebe/constants/codon_tables.rb +77 -0
- data/lib/bioroebe/constants/database_constants.rb +107 -0
- data/lib/bioroebe/constants/files_and_directories.rb +579 -0
- data/lib/bioroebe/constants/misc.rb +189 -0
- data/lib/bioroebe/constants/newline.rb +14 -0
- data/lib/bioroebe/constants/nucleotides.rb +114 -0
- data/lib/bioroebe/constants/regex.rb +28 -0
- data/lib/bioroebe/constants/roebe.rb +38 -0
- data/lib/bioroebe/constants/row_terminator.rb +16 -0
- data/lib/bioroebe/constants/tabulator.rb +14 -0
- data/lib/bioroebe/constants/unicode.rb +12 -0
- data/lib/bioroebe/constants/urls.rb +50 -0
- data/lib/bioroebe/conversions/README.md +3 -0
- data/lib/bioroebe/conversions/convert_aminoacid_to_dna.rb +298 -0
- data/lib/bioroebe/conversions/dna_to_aminoacid_sequence.rb +569 -0
- data/lib/bioroebe/count/README.md +1 -0
- data/lib/bioroebe/count/count_amount_of_aminoacids.rb +352 -0
- data/lib/bioroebe/count/count_amount_of_nucleotides.rb +491 -0
- data/lib/bioroebe/count/count_at.rb +39 -0
- data/lib/bioroebe/count/count_gc.rb +43 -0
- data/lib/bioroebe/css/README.md +5 -0
- data/lib/bioroebe/css/project.css +121 -0
- data/lib/bioroebe/data/README.md +10 -0
- data/lib/bioroebe/data/bam/README.md +1 -0
- data/lib/bioroebe/data/data.txt +192 -0
- data/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta +12 -0
- data/lib/bioroebe/data/fasta/alu_elements.fasta +42 -0
- data/lib/bioroebe/data/fasta/lady_slippers_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/loxP.fasta +2 -0
- data/lib/bioroebe/data/fasta/ls_orchid.fasta +1197 -0
- data/lib/bioroebe/data/fasta/pax6_in_mouse.fasta +1 -0
- data/lib/bioroebe/data/fasta/test.fasta +7 -0
- data/lib/bioroebe/data/fasta/test_DNA.fasta +1 -0
- data/lib/bioroebe/data/fastq/fastq_example_file.fastq +32 -0
- data/lib/bioroebe/data/fastq/fastq_example_file_SP1.fastq +1000 -0
- data/lib/bioroebe/data/fastq/one_random_fastq_entry.fastq +4 -0
- data/lib/bioroebe/data/genbank/sample_file.genbank +15 -0
- data/lib/bioroebe/data/genbank/standard.fasta +3 -0
- data/lib/bioroebe/data/gff/Escherichia_coli_K12_plasmid_F_DNA_NC_002483.1.gff3 +345 -0
- data/lib/bioroebe/data/gff/sample.gff +2 -0
- data/lib/bioroebe/data/gff/test_gene.gff +4 -0
- data/lib/bioroebe/data/gff/transcripts.gff +16 -0
- data/lib/bioroebe/data/gtf/README.md +1 -0
- data/lib/bioroebe/data/json/example_config.json +48 -0
- data/lib/bioroebe/data/pdb/1VII.pdb +754 -0
- data/lib/bioroebe/data/pdb/ala_phe_ala.pdb +228 -0
- data/lib/bioroebe/data/pdb/rcsb_pdb_1VII.fasta +2 -0
- data/lib/bioroebe/data/phylip/README.md +11 -0
- data/lib/bioroebe/data/phylip/example.phylip +7 -0
- data/lib/bioroebe/data/svg/example.svg +301 -0
- data/lib/bioroebe/databases/README.md +1 -0
- data/lib/bioroebe/databases/download_taxonomy_database.rb +102 -0
- data/lib/bioroebe/dotplots/README.md +5 -0
- data/lib/bioroebe/dotplots/advanced_dotplot.rb +256 -0
- data/lib/bioroebe/dotplots/dotplot.rb +184 -0
- data/lib/bioroebe/electron_microscopy/coordinate_analyzer.rb +191 -0
- data/lib/bioroebe/electron_microscopy/fix_pos_file.rb +102 -0
- data/lib/bioroebe/electron_microscopy/generate_em2em_file.rb +122 -0
- data/lib/bioroebe/electron_microscopy/parse_coordinates.rb +197 -0
- data/lib/bioroebe/electron_microscopy/read_file_xmd.rb +282 -0
- data/lib/bioroebe/electron_microscopy/simple_star_file_generator.rb +131 -0
- data/lib/bioroebe/encoding/README.md +2 -0
- data/lib/bioroebe/encoding/encoding.rb +45 -0
- data/lib/bioroebe/enzymes/README.md +2 -0
- data/lib/bioroebe/enzymes/has_this_restriction_enzyme.rb +46 -0
- data/lib/bioroebe/enzymes/restriction_enzyme.rb +200 -0
- data/lib/bioroebe/enzymes/restriction_enzymes_file.rb +72 -0
- data/lib/bioroebe/enzymes/return_restriction_enzyme_sequence_and_cut_position.rb +80 -0
- data/lib/bioroebe/enzymes/return_sequence_that_is_cut_via_restriction_enzyme.rb +65 -0
- data/lib/bioroebe/enzymes/show_restriction_enzymes.rb +119 -0
- data/lib/bioroebe/exceptions/README.md +2 -0
- data/lib/bioroebe/exceptions/exceptions.rb +17 -0
- data/lib/bioroebe/ext/LICENCE.md +5 -0
- data/lib/bioroebe/ext/README.md +7 -0
- data/lib/bioroebe/ext/main.cpp +45 -0
- data/lib/bioroebe/ext/nucleotide.cpp +24 -0
- data/lib/bioroebe/ext/nussinov_algorithm.cpp +348 -0
- data/lib/bioroebe/ext/sequence +0 -0
- data/lib/bioroebe/ext/sequence.cpp +162 -0
- data/lib/bioroebe/fasta_and_fastq/README.md +6 -0
- data/lib/bioroebe/fasta_and_fastq/autocorrect_the_name_of_this_fasta_file.rb +88 -0
- data/lib/bioroebe/fasta_and_fastq/compact_fasta_file/compact_fasta_file.rb +151 -0
- data/lib/bioroebe/fasta_and_fastq/display_how_many_fasta_entries_are_in_this_directory.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/download_fasta.rb +248 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/README.md +2 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_defline/fasta_defline.rb +113 -0
- data/lib/bioroebe/fasta_and_fastq/fasta_parser.rb +167 -0
- data/lib/bioroebe/fasta_and_fastq/fastq_format_explainer.rb +131 -0
- data/lib/bioroebe/fasta_and_fastq/length_modifier/length_modifier.rb +87 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/constants.rb +50 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/initialize.rb +86 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/menu.rb +117 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/misc.rb +981 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb +27 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/report.rb +156 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/reset.rb +128 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fasta/run.rb +20 -0
- data/lib/bioroebe/fasta_and_fastq/parse_fastq/parse_fastq.rb +83 -0
- data/lib/bioroebe/fasta_and_fastq/return_fasta_subsection_of_this_file.rb +112 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_headers.rb +135 -0
- data/lib/bioroebe/fasta_and_fastq/show_fasta_statistics.rb +188 -0
- data/lib/bioroebe/fasta_and_fastq/simplify_fasta_header/simplify_fasta_header.rb +111 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/constants.rb +26 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/menu.rb +41 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/misc.rb +23 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/reset.rb +68 -0
- data/lib/bioroebe/fasta_and_fastq/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb +290 -0
- data/lib/bioroebe/genbank/README.md +1 -0
- data/lib/bioroebe/genbank/genbank_flat_file_format_generator.rb +275 -0
- data/lib/bioroebe/genbank/genbank_parser.rb +291 -0
- data/lib/bioroebe/gene/gene.rb +64 -0
- data/lib/bioroebe/genomes/genome_pattern.rb +165 -0
- data/lib/bioroebe/genomes/genome_retriever.rb +79 -0
- data/lib/bioroebe/gui/experimental/README.md +1 -0
- data/lib/bioroebe/gui/experimental/snapgene/snapgene.rb +147 -0
- data/lib/bioroebe/gui/gtk3/README.md +2 -0
- data/lib/bioroebe/gui/gtk3/alignment/alignment.rb +337 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb +510 -0
- data/lib/bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb +55 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.config +6 -0
- data/lib/bioroebe/gui/gtk3/anti_sense_strand/anti_sense_strand.rb +29 -0
- data/lib/bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb +196 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.config +6 -0
- data/lib/bioroebe/gui/gtk3/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +106 -0
- data/lib/bioroebe/gui/gtk3/controller/controller.rb +406 -0
- data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +609 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config +6 -0
- data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +189 -0
- data/lib/bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb +245 -0
- data/lib/bioroebe/gui/gtk3/format_converter/format_converter.rb +346 -0
- data/lib/bioroebe/gui/gtk3/gene/gene.rb +182 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb +370 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.config +6 -0
- data/lib/bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb +175 -0
- data/lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb +428 -0
- data/lib/bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb +342 -0
- data/lib/bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb +580 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.config +6 -0
- data/lib/bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb +182 -0
- data/lib/bioroebe/gui/gtk3/random_sequence/random_sequence.rb +566 -0
- data/lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.config +6 -0
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- data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb +556 -0
- data/lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb +171 -0
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- data/lib/bioroebe/gui/libui/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb +60 -0
- data/lib/bioroebe/gui/libui/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb +161 -0
- data/lib/bioroebe/gui/libui/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb +76 -0
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- data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb +216 -0
- data/lib/bioroebe/gui/shared_code/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget_module.rb +284 -0
- data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb +402 -0
- data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb +192 -0
- data/lib/bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb +72 -0
- data/lib/bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb +213 -0
- data/lib/bioroebe/gui/tk/aminoacid_composition/aminoacid_composition.rb +206 -0
- data/lib/bioroebe/gui/tk/blosum_matrix_viewer/blosum_matrix_viewer.rb +140 -0
- data/lib/bioroebe/gui/tk/hamming_distance/hamming_distance.rb +262 -0
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- data/lib/bioroebe/gui/tk/three_to_one/three_to_one.rb +199 -0
- data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb +519 -0
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- data/lib/bioroebe/nucleotides/show_nucleotide_sequence.rb +556 -0
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- data/lib/bioroebe/palindromes/palindrome_finder.rb +208 -0
- data/lib/bioroebe/palindromes/palindrome_generator.rb +272 -0
- data/lib/bioroebe/parsers/biolang_parser.rb +156 -0
- data/lib/bioroebe/parsers/blosum_parser.rb +222 -0
- data/lib/bioroebe/parsers/genbank_parser.rb +78 -0
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- data/lib/bioroebe/patterns/analyse_glycosylation_pattern.rb +149 -0
- data/lib/bioroebe/patterns/is_this_sequence_a_EGF2_pattern.rb +66 -0
- data/lib/bioroebe/patterns/profile_pattern.rb +182 -0
- data/lib/bioroebe/patterns/rgg_scanner.rb +160 -0
- data/lib/bioroebe/patterns/scan_for_repeat.rb +157 -0
- data/lib/bioroebe/pdb/download_this_pdb.rb +67 -0
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- data/lib/bioroebe/pdb/report_secondary_structures_from_this_pdb_file.rb +225 -0
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- data/lib/bioroebe/project/project.rb +264 -0
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- data/lib/bioroebe/regexes/README.md +2 -0
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- data/lib/bioroebe/toplevel_methods/calculate_n50_value.rb +57 -0
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- data/lib/bioroebe/toplevel_methods/complement.rb +58 -0
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- data/lib/bioroebe/toplevel_methods/leading_five_prime_and_trailing_three_prime.rb +101 -0
- data/lib/bioroebe/toplevel_methods/levensthein.rb +63 -0
- data/lib/bioroebe/toplevel_methods/log_directory.rb +109 -0
- data/lib/bioroebe/toplevel_methods/longest_common_substring.rb +55 -0
- data/lib/bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb +88 -0
- data/lib/bioroebe/toplevel_methods/matches.rb +259 -0
- data/lib/bioroebe/toplevel_methods/misc.rb +432 -0
- data/lib/bioroebe/toplevel_methods/nucleotides.rb +715 -0
- data/lib/bioroebe/toplevel_methods/number_of_clones.rb +63 -0
- data/lib/bioroebe/toplevel_methods/open_in_browser.rb +77 -0
- data/lib/bioroebe/toplevel_methods/open_reading_frames.rb +236 -0
- data/lib/bioroebe/toplevel_methods/opn.rb +34 -0
- data/lib/bioroebe/toplevel_methods/palindromes.rb +127 -0
- data/lib/bioroebe/toplevel_methods/parse.rb +59 -0
- data/lib/bioroebe/toplevel_methods/phred_error_probability.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rds.rb +24 -0
- data/lib/bioroebe/toplevel_methods/remove.rb +86 -0
- data/lib/bioroebe/toplevel_methods/return_source_code_of_this_method.rb +35 -0
- data/lib/bioroebe/toplevel_methods/return_subsequence_based_on_indices.rb +68 -0
- data/lib/bioroebe/toplevel_methods/rna_splicing.rb +73 -0
- data/lib/bioroebe/toplevel_methods/rnalfold.rb +69 -0
- data/lib/bioroebe/toplevel_methods/searching_and_finding.rb +116 -0
- data/lib/bioroebe/toplevel_methods/shuffleseq.rb +37 -0
- data/lib/bioroebe/toplevel_methods/statistics.rb +53 -0
- data/lib/bioroebe/toplevel_methods/sum_of_odd_integers.rb +62 -0
- data/lib/bioroebe/toplevel_methods/taxonomy.rb +187 -0
- data/lib/bioroebe/toplevel_methods/three_delimiter.rb +34 -0
- data/lib/bioroebe/toplevel_methods/time_and_date.rb +53 -0
- data/lib/bioroebe/toplevel_methods/to_camelcase.rb +26 -0
- data/lib/bioroebe/toplevel_methods/truncate.rb +48 -0
- data/lib/bioroebe/toplevel_methods/url.rb +36 -0
- data/lib/bioroebe/toplevel_methods/verbose.rb +59 -0
- data/lib/bioroebe/utility_scripts/align_open_reading_frames.rb +191 -0
- data/lib/bioroebe/utility_scripts/analyse_local_dataset.rb +119 -0
- data/lib/bioroebe/utility_scripts/check_for_mismatches/check_for_mismatches.rb +230 -0
- data/lib/bioroebe/utility_scripts/compacter.rb +131 -0
- data/lib/bioroebe/utility_scripts/compseq/compseq.rb +529 -0
- data/lib/bioroebe/utility_scripts/consensus_sequence.rb +374 -0
- data/lib/bioroebe/utility_scripts/create_batch_entrez_file.rb +130 -0
- data/lib/bioroebe/utility_scripts/determine_antigenic_areas.rb +115 -0
- data/lib/bioroebe/utility_scripts/determine_missing_nucleotides_percentage.rb +137 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/determine.rb +73 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb +31 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/initialize.rb +37 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/menu.rb +49 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/misc.rb +471 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/report.rb +113 -0
- data/lib/bioroebe/utility_scripts/display_open_reading_frames/reset.rb +56 -0
- data/lib/bioroebe/utility_scripts/dot_alignment.rb +177 -0
- data/lib/bioroebe/utility_scripts/download_files_from_rebase.rb +72 -0
- data/lib/bioroebe/utility_scripts/find_gene.rb +202 -0
- data/lib/bioroebe/utility_scripts/mirror_repeat.rb +235 -0
- data/lib/bioroebe/utility_scripts/move_file_to_its_correct_location.rb +151 -0
- data/lib/bioroebe/utility_scripts/parse_taxonomy.rb +168 -0
- data/lib/bioroebe/utility_scripts/pathways.rb +152 -0
- data/lib/bioroebe/utility_scripts/permutations.rb +145 -0
- data/lib/bioroebe/utility_scripts/punnet/punnet.rb +126 -0
- data/lib/bioroebe/utility_scripts/show_this_dna_sequence.rb +148 -0
- data/lib/bioroebe/utility_scripts/showorf/constants.rb +36 -0
- data/lib/bioroebe/utility_scripts/showorf/help.rb +33 -0
- data/lib/bioroebe/utility_scripts/showorf/initialize.rb +52 -0
- data/lib/bioroebe/utility_scripts/showorf/menu.rb +68 -0
- data/lib/bioroebe/utility_scripts/showorf/reset.rb +39 -0
- data/lib/bioroebe/utility_scripts/showorf/run.rb +152 -0
- data/lib/bioroebe/utility_scripts/showorf/show.rb +97 -0
- data/lib/bioroebe/utility_scripts/showorf/showorf.rb +488 -0
- data/lib/bioroebe/version/version.rb +44 -0
- data/lib/bioroebe/viennarna/README.md +3 -0
- data/lib/bioroebe/viennarna/rnafold_wrapper.rb +196 -0
- data/lib/bioroebe/with_gui.rb +18 -0
- data/lib/bioroebe/www/bioroebe.cgi +44 -0
- data/lib/bioroebe/www/embeddable_interface.rb +686 -0
- data/lib/bioroebe/www/sinatra/sinatra.rb +1013 -0
- data/lib/bioroebe/yaml/agarose/agarose_concentrations.yml +21 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids.yml +92 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_abbreviations.yml +31 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_average_mass_table.yml +33 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_classification.yml +18 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_english.yml +26 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_frequency.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_long_name_to_one_letter.yml +61 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_molecular_formula.yml +32 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_monoisotopic_mass_table.yml +38 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_reste.yml +35 -0
- data/lib/bioroebe/yaml/aminoacids/amino_acids_three_to_one.yml +34 -0
- data/lib/bioroebe/yaml/aminoacids/hydropathy_table.yml +44 -0
- data/lib/bioroebe/yaml/aminoacids/molecular_weight.yml +29 -0
- data/lib/bioroebe/yaml/aminoacids/simple_aminoacids.yml +66 -0
- data/lib/bioroebe/yaml/aminoacids/weight_of_common_proteins.yml +33 -0
- data/lib/bioroebe/yaml/antisense/antisense.yml +9 -0
- data/lib/bioroebe/yaml/base_composition_of_dna.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum45.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum50.yml +34 -0
- data/lib/bioroebe/yaml/blosum/blosum62.yml +35 -0
- data/lib/bioroebe/yaml/blosum/blosum80.yml +37 -0
- data/lib/bioroebe/yaml/blosum/blosum90.yml +36 -0
- data/lib/bioroebe/yaml/blosum/blosum_matrix.yml +200 -0
- data/lib/bioroebe/yaml/chromosomes/chromosome_numbers.yml +30 -0
- data/lib/bioroebe/yaml/codon_tables/1.yml +113 -0
- data/lib/bioroebe/yaml/codon_tables/10.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/11.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/12.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/13.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/14.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/15.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/16.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/2.yml +86 -0
- data/lib/bioroebe/yaml/codon_tables/21.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/22.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/23.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/24.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/25.yml +89 -0
- data/lib/bioroebe/yaml/codon_tables/26.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/27.yml +104 -0
- data/lib/bioroebe/yaml/codon_tables/28.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/29.yml +93 -0
- data/lib/bioroebe/yaml/codon_tables/3.yml +98 -0
- data/lib/bioroebe/yaml/codon_tables/30.yml +91 -0
- data/lib/bioroebe/yaml/codon_tables/31.yml +94 -0
- data/lib/bioroebe/yaml/codon_tables/33.yml +101 -0
- data/lib/bioroebe/yaml/codon_tables/4.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/5.yml +100 -0
- data/lib/bioroebe/yaml/codon_tables/6.yml +96 -0
- data/lib/bioroebe/yaml/codon_tables/9.yml +97 -0
- data/lib/bioroebe/yaml/codon_tables/overview.yml +42 -0
- data/lib/bioroebe/yaml/configuration/README.md +12 -0
- data/lib/bioroebe/yaml/configuration/browser.yml +1 -0
- data/lib/bioroebe/yaml/configuration/colourize_fasta_sequences.yml +14 -0
- data/lib/bioroebe/yaml/configuration/default_colours_for_the_aminoacids.yml +28 -0
- data/lib/bioroebe/yaml/configuration/temp_dir.yml +1 -0
- data/lib/bioroebe/yaml/configuration/try_to_use_matplotlib.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_opn.yml +1 -0
- data/lib/bioroebe/yaml/configuration/use_this_database.yml +1 -0
- data/lib/bioroebe/yaml/create_these_directories_on_startup/create_these_directories_on_startup.yml +9 -0
- data/lib/bioroebe/yaml/default_dna_input.yml +3 -0
- data/lib/bioroebe/yaml/enzymes/enzyme_classes.yml +15 -0
- data/lib/bioroebe/yaml/enzymes/pH-Optima.yml +11 -0
- data/lib/bioroebe/yaml/fasta_and_fastq/fastq_quality_schemes.yml +44 -0
- data/lib/bioroebe/yaml/genomes/README.md +16 -0
- data/lib/bioroebe/yaml/humans/README.md +2 -0
- data/lib/bioroebe/yaml/humans/human_chromosomes.yml +53 -0
- data/lib/bioroebe/yaml/laboratory/README.md +1 -0
- data/lib/bioroebe/yaml/laboratory/pipettes.yml +8 -0
- data/lib/bioroebe/yaml/mRNA/mRNA.yml +16 -0
- data/lib/bioroebe/yaml/nuclear_localization_sequences.yml +15 -0
- data/lib/bioroebe/yaml/nucleotides/abbreviations_for_nucleotides.yml +29 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotide_density.yml +10 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides.yml +34 -0
- data/lib/bioroebe/yaml/nucleotides/nucleotides_weight.yml +12 -0
- data/lib/bioroebe/yaml/pathways/README.md +2 -0
- data/lib/bioroebe/yaml/pathways/citric_acid_cycle.yml +16 -0
- data/lib/bioroebe/yaml/pathways/glycolysis.yml +20 -0
- data/lib/bioroebe/yaml/pathways/shikimate_pathway.yml +23 -0
- data/lib/bioroebe/yaml/pathways/urea_cycle.yml +11 -0
- data/lib/bioroebe/yaml/primers/README.md +4 -0
- data/lib/bioroebe/yaml/primers/primers.yml +3 -0
- data/lib/bioroebe/yaml/promoters/35S.yml +15 -0
- data/lib/bioroebe/yaml/promoters/strong_promoters.yml +24 -0
- data/lib/bioroebe/yaml/proteases/proteases.yml +3 -0
- data/lib/bioroebe/yaml/proteins/ubiquitin.yml +4 -0
- data/lib/bioroebe/yaml/remote_urls/README.md +4 -0
- data/lib/bioroebe/yaml/remote_urls/remote_urls.yml +3 -0
- data/lib/bioroebe/yaml/restriction_enzymes/restriction_enzymes.yml +630 -0
- data/lib/bioroebe/yaml/sequences/JX472995_Green_fluorescent_protein_from_Aequorea_victoria.fasta +14 -0
- data/lib/bioroebe/yaml/sequences/README.md +2 -0
- data/lib/bioroebe/yaml/talens.yml +22 -0
- data/lib/bioroebe/yaml/viruses/ecoli_phages.yml +63 -0
- data/lib/bioroebe/yaml/viruses/viruses.yml +6 -0
- data/lib/bioroebe.rb +5 -0
- data/spec/testing_toplevel_method_editor.rb +20 -0
- data/spec/testing_toplevel_method_url.rb +15 -0
- data/spec/testing_toplevel_method_verbose.rb +13 -0
- data/test/advanced_svg_example.rb +307 -0
- data/test/testing_bioroebe.rb +25 -0
- data/test/testing_codons.rb +45 -0
- data/test/testing_dna_to_rna_conversion.rb +15 -0
- data/test/testing_parse_pdb_file.rb +23 -0
- data/test/testing_reverse_complement.rb +32 -0
- data/test/testing_svg_component_of_bioroebe.rb +311 -0
- data/test/testing_svg_component_of_bioroebe_from_json_dataset.rb +34 -0
- data/test/testing_taxonomy.rb +22 -0
- metadata +1059 -0
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# === create_button (buttons tag, button tag)
|
162
|
+
# ========================================================================= #
|
163
|
+
def create_button
|
164
|
+
# ======================================================================= #
|
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|
+
# === @button_convert
|
166
|
+
# ======================================================================= #
|
167
|
+
@button_convert = gtk_button('_Convert')
|
168
|
+
@button_convert.hint = 'Click this button in order to <b>convert the '\
|
169
|
+
'three amino acids code to a one amino acid '\
|
170
|
+
'letter code</b>. This is the <b>default</b>.'\
|
171
|
+
'If you need to convert from the one-letter code '\
|
172
|
+
'to the three-letter code then you need to use the '\
|
173
|
+
'check button on the right side.'
|
174
|
+
@button_convert.disallow_resizing
|
175
|
+
@button_convert.set_size_request(350, 40)
|
176
|
+
@button_convert.on_clicked {
|
177
|
+
do_trigger_the_conversion
|
178
|
+
}
|
179
|
+
@button_convert.clear_background
|
180
|
+
@button_convert.on_hover(:lightblue)
|
181
|
+
@button_convert.set_name('button1')
|
182
|
+
end
|
183
|
+
|
184
|
+
# ========================================================================= #
|
185
|
+
# === run (run tag)
|
186
|
+
# ========================================================================= #
|
187
|
+
def run
|
188
|
+
create_skeleton_then_connect_skeleton
|
189
|
+
end
|
190
|
+
|
191
|
+
# ========================================================================= #
|
192
|
+
# === connect_skeleton (connect tag)
|
193
|
+
# ========================================================================= #
|
194
|
+
def connect_skeleton
|
195
|
+
abort_on_exception
|
196
|
+
_ = text('Input sequence:')
|
197
|
+
_.hint = 'Input your three-letter-aminoacid sequence below.'
|
198
|
+
minimal(_, 2)
|
199
|
+
@entry1.on_enter_key_pressed {
|
200
|
+
do_trigger_the_conversion(@entry1.text?)
|
201
|
+
}
|
202
|
+
minimal(@entry1, 4)
|
203
|
+
minimal(@entry2, 4)
|
204
|
+
hbox = gtk_hbox
|
205
|
+
hbox.maximal(
|
206
|
+
gtk_button_box(@button_convert) { :spread }, 2
|
207
|
+
)
|
208
|
+
hbox.minimal(
|
209
|
+
return_the_checkbox_widget, 2
|
210
|
+
)
|
211
|
+
minimal(hbox, 4)
|
212
|
+
end
|
213
|
+
|
214
|
+
# ========================================================================= #
|
215
|
+
# === Bioroebe::GUI::Gtk::ThreeToOne.run
|
216
|
+
# ========================================================================= #
|
217
|
+
def self.run(
|
218
|
+
i = ARGV
|
219
|
+
)
|
220
|
+
require 'gtk_paradise/run'
|
221
|
+
_ = ::Bioroebe::GUI::Gtk::ThreeToOne.new(i)
|
222
|
+
r = ::Gtk.run
|
223
|
+
r << _
|
224
|
+
r.automatic_size_then_automatic_title
|
225
|
+
r.top_left_then_run
|
226
|
+
end
|
227
|
+
|
228
|
+
# ========================================================================= #
|
229
|
+
# === do_trigger_the_conversion (conversion tag)
|
230
|
+
#
|
231
|
+
# This method is the one that will convert from the three-letter to the
|
232
|
+
# one-letter and vice versa.
|
233
|
+
# ========================================================================= #
|
234
|
+
def do_trigger_the_conversion(
|
235
|
+
i = @entry1.text?,
|
236
|
+
checkbox1 = @checkbox1
|
237
|
+
)
|
238
|
+
i = i.to_s.dup.delete(' ')
|
239
|
+
if checkbox1.active?
|
240
|
+
new_result = Bioroebe.three_to_one(i).to_s
|
241
|
+
else
|
242
|
+
new_result = Bioroebe.one_to_three(i).to_s
|
243
|
+
end
|
244
|
+
if new_result and !new_result.empty?
|
245
|
+
@entry2.set_text(new_result)
|
246
|
+
@entry2.make_bold
|
247
|
+
end
|
248
|
+
end; alias do_the_conversion do_trigger_the_conversion # === do_the_conversion
|
249
|
+
|
250
|
+
# ========================================================================= #
|
251
|
+
# === create_entries (entries tag)
|
252
|
+
# ========================================================================= #
|
253
|
+
def create_entries
|
254
|
+
# ======================================================================= #
|
255
|
+
# === @entry1
|
256
|
+
# ======================================================================= #
|
257
|
+
@entry1 = gtk_entry
|
258
|
+
@entry1.hint = 'This entry should contain the three-letter code '\
|
259
|
+
'for the input sequence, such as "Asp-Lys-Gln", without '\
|
260
|
+
'the quotes. Use the <b>enter key</b> to trigger the '\
|
261
|
+
'conversion, or use the button below.'
|
262
|
+
@entry1.on_enter { do_the_conversion }
|
263
|
+
# ======================================================================= #
|
264
|
+
# === @entry2
|
265
|
+
# ======================================================================= #
|
266
|
+
@entry2 = gtk_entry
|
267
|
+
@entry2.the_user_may_not_modify_this_entry
|
268
|
+
@entry2.hint = 'This input field will display the result of the '\
|
269
|
+
'conversion. The user can not modify it.'
|
270
|
+
@entry2.css_class('tomato')
|
271
|
+
@entry2.make_bold
|
272
|
+
# @entry2.on_click_select_everything
|
273
|
+
end
|
274
|
+
|
275
|
+
end; end; end; end
|
276
|
+
|
277
|
+
if __FILE__ == $PROGRAM_NAME
|
278
|
+
Bioroebe::GUI::Gtk::ThreeToOne.run
|
279
|
+
end
|
@@ -0,0 +1,23 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::GUI::Gtk::ThreeToOne
|
6
|
+
# =========================================================================== #
|
7
|
+
# require 'bioroebe/gui/gtk3/three_to_one/title.rb'
|
8
|
+
# Bioroebe::GUI::Gtk::ThreeToOne::TITLE
|
9
|
+
# =========================================================================== #
|
10
|
+
module Bioroebe
|
11
|
+
|
12
|
+
module GUI
|
13
|
+
|
14
|
+
module Gtk
|
15
|
+
|
16
|
+
module ThreeToOneModule
|
17
|
+
|
18
|
+
# ========================================================================= #
|
19
|
+
# === Bioroebe::GUI::Gtk::ThreeToOneModule::TITLE
|
20
|
+
# ========================================================================= #
|
21
|
+
TITLE = 'Three aminoacids to one aminoacid converter'
|
22
|
+
|
23
|
+
end; end; end; end
|
@@ -0,0 +1,368 @@
|
|
1
|
+
#!/usr/bin/ruby -w
|
2
|
+
# Encoding: UTF-8
|
3
|
+
# frozen_string_literal: true
|
4
|
+
# =========================================================================== #
|
5
|
+
# === Bioroebe::GUI::Gtk::WwwFinder
|
6
|
+
#
|
7
|
+
# This small widget can be used to "generate" random aminoacids quickly.
|
8
|
+
# =========================================================================== #
|
9
|
+
# require 'bioroebe/gui/gtk3/gtk3_standalone/gtk3_standalone.rb'
|
10
|
+
# Bioroebe::GUI::Gtk::WwwFinder.run
|
11
|
+
# =========================================================================== #
|
12
|
+
require 'gtk_paradise/require_gtk3'
|
13
|
+
|
14
|
+
module Bioroebe
|
15
|
+
|
16
|
+
module GUI
|
17
|
+
|
18
|
+
module Gtk
|
19
|
+
|
20
|
+
class WwwFinder < ::Gtk::Box # === Bioroebe::GUI::Gtk::WwwFinder
|
21
|
+
|
22
|
+
begin
|
23
|
+
require 'open'
|
24
|
+
rescue LoadError; end
|
25
|
+
|
26
|
+
begin
|
27
|
+
require 'colours'
|
28
|
+
include ::Colours
|
29
|
+
rescue LoadError; end
|
30
|
+
|
31
|
+
require 'bioroebe/constants/GUIs.rb'
|
32
|
+
include ::Bioroebe::GUI
|
33
|
+
|
34
|
+
require 'gtk_paradise/requires/require_the_base_module.rb'
|
35
|
+
include ::Gtk::BaseModule
|
36
|
+
|
37
|
+
# ========================================================================= #
|
38
|
+
# === NAMESPACE
|
39
|
+
# ========================================================================= #
|
40
|
+
NAMESPACE = inspect
|
41
|
+
|
42
|
+
# ========================================================================= #
|
43
|
+
# === TITLE
|
44
|
+
# ========================================================================= #
|
45
|
+
TITLE = 'WWW-Finder'
|
46
|
+
|
47
|
+
# ========================================================================= #
|
48
|
+
# === BASE_URL_FOR_DBGET
|
49
|
+
# ========================================================================= #
|
50
|
+
BASE_URL_FOR_DBGET =
|
51
|
+
'"https://www.genome.ad.jp/dbget-bin/www_bfind_sub?mode=bfind&max_hit=1200&dbkey=kegg&keywords='.dup
|
52
|
+
|
53
|
+
# ========================================================================= #
|
54
|
+
# === BASE_URL_FOR_NCBI
|
55
|
+
# ========================================================================= #
|
56
|
+
BASE_URL_FOR_NCBI =
|
57
|
+
'"https://www.ncbi.nlm.nih.gov/gquery/gquery.fcgi?term='
|
58
|
+
|
59
|
+
# ========================================================================= #
|
60
|
+
# === WIDTH
|
61
|
+
# ========================================================================= #
|
62
|
+
WIDTH = 580
|
63
|
+
|
64
|
+
# ========================================================================= #
|
65
|
+
# === HEIGHT
|
66
|
+
# ========================================================================= #
|
67
|
+
HEIGHT = 720
|
68
|
+
|
69
|
+
# ========================================================================= #
|
70
|
+
# === USE_THIS_FONT
|
71
|
+
# ========================================================================= #
|
72
|
+
USE_THIS_FONT = :dejavu_condensed_22
|
73
|
+
|
74
|
+
# ========================================================================= #
|
75
|
+
# === initialize
|
76
|
+
# ========================================================================= #
|
77
|
+
def initialize(
|
78
|
+
commandline_arguments = ARGV,
|
79
|
+
run_already = true
|
80
|
+
)
|
81
|
+
super(:vertical)
|
82
|
+
register_sigint
|
83
|
+
reset
|
84
|
+
set_commandline_arguments(
|
85
|
+
commandline_arguments
|
86
|
+
)
|
87
|
+
run if run_already
|
88
|
+
end
|
89
|
+
|
90
|
+
# ========================================================================= #
|
91
|
+
# === reset (reset tag)
|
92
|
+
# ========================================================================= #
|
93
|
+
def reset
|
94
|
+
reset_the_internal_variables
|
95
|
+
# ======================================================================= #
|
96
|
+
# === @configuration
|
97
|
+
# ======================================================================= #
|
98
|
+
@configuration = [true, __dir__, NAMESPACE]
|
99
|
+
title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
|
100
|
+
use_gtk_paradise_project_css_file
|
101
|
+
append_project_css_file
|
102
|
+
infer_the_size_automatically
|
103
|
+
# ======================================================================= #
|
104
|
+
# === @button_quit
|
105
|
+
# ======================================================================= #
|
106
|
+
@button_quit = ''
|
107
|
+
# ======================================================================= #
|
108
|
+
# === @v_box
|
109
|
+
# ======================================================================= #
|
110
|
+
@v_box = gtk_vbox
|
111
|
+
background_colour :slateblue
|
112
|
+
end
|
113
|
+
|
114
|
+
# ========================================================================= #
|
115
|
+
# === padding?
|
116
|
+
# ========================================================================= #
|
117
|
+
def padding?
|
118
|
+
4
|
119
|
+
end
|
120
|
+
|
121
|
+
# ========================================================================= #
|
122
|
+
# === border_size?
|
123
|
+
# ========================================================================= #
|
124
|
+
def border_size?
|
125
|
+
0
|
126
|
+
end
|
127
|
+
|
128
|
+
# ========================================================================= #
|
129
|
+
# === create_skeleton (create tag)
|
130
|
+
# ========================================================================= #
|
131
|
+
def create_skeleton
|
132
|
+
create_menu
|
133
|
+
create_check_boxes
|
134
|
+
create_entries
|
135
|
+
create_buttons
|
136
|
+
create_vbox
|
137
|
+
end
|
138
|
+
|
139
|
+
# ========================================================================= #
|
140
|
+
# === create_menu
|
141
|
+
#
|
142
|
+
# This creates the menu.
|
143
|
+
# ========================================================================= #
|
144
|
+
def create_menu
|
145
|
+
begin
|
146
|
+
require 'gtk_paradise/widgets/version_agnostic/my_image_menu_item.rb'
|
147
|
+
rescue LoadError => error
|
148
|
+
pp error
|
149
|
+
end
|
150
|
+
@menu_bar = gtk_menu_bar
|
151
|
+
@menu_item = gtk_menu_item('Menu')
|
152
|
+
@first_submenu = gtk_menu
|
153
|
+
@item1 = image_menu_item('foo',nil,0)
|
154
|
+
@item1.signal_connect(:activate) { do_something }
|
155
|
+
@first_submenu << @item1
|
156
|
+
@item2 = image_menu_item('bar',nil,3)
|
157
|
+
@item2.signal_connect(:activate) { e 'test 2' }
|
158
|
+
@first_submenu << @item2
|
159
|
+
@menu_item.set_submenu(@first_submenu)
|
160
|
+
@menu_bar.append(@menu_item)
|
161
|
+
end
|
162
|
+
|
163
|
+
# ========================================================================= #
|
164
|
+
# === create_check_boxes
|
165
|
+
#
|
166
|
+
# Creates the check boxes. On startup, we synchronize this.
|
167
|
+
# ========================================================================= #
|
168
|
+
def create_check_boxes
|
169
|
+
@checkbox_synchronize = check_button('Synchronize On', false)
|
170
|
+
@checkbox_synchronize.set_active(true)
|
171
|
+
end
|
172
|
+
|
173
|
+
# ========================================================================= #
|
174
|
+
# === create_entries
|
175
|
+
#
|
176
|
+
# entries tag.
|
177
|
+
# ========================================================================= #
|
178
|
+
def create_entries
|
179
|
+
@entry_dbget = create_entry_with_text_and_max_length('alzheimer')
|
180
|
+
# ======================================================================= #
|
181
|
+
# ensembl entry
|
182
|
+
# ======================================================================= #
|
183
|
+
@entry_ensembl = create_entry_with_text_and_max_length('helicobacter')
|
184
|
+
# ======================================================================= #
|
185
|
+
# ncbi entry
|
186
|
+
# ======================================================================= #
|
187
|
+
@entry_ncbi = create_entry_with_text_and_max_length('escherichia coli')
|
188
|
+
# ======================================================================= #
|
189
|
+
# === @entry_nih
|
190
|
+
#
|
191
|
+
# nih entry
|
192
|
+
# ======================================================================= #
|
193
|
+
@entry_nih = create_entry_with_text_and_max_length('escherichia coli')
|
194
|
+
# A helper array containing all our gtk-entries for this application.
|
195
|
+
@array_entries = [
|
196
|
+
@entry_dbget, @entry_ensembl, @entry_ncbi, @entry_nih
|
197
|
+
]
|
198
|
+
@array_entries.each { |entry|
|
199
|
+
entry.signal_connect(:changed) { |w, event|
|
200
|
+
if @checkbox_synchronize.active?
|
201
|
+
@array_entries.each { |entry|
|
202
|
+
entry.set_text(entry.text) unless e == entry
|
203
|
+
}
|
204
|
+
end
|
205
|
+
}
|
206
|
+
entry.signal_connect(:activate) { |w| puts w }
|
207
|
+
}
|
208
|
+
end
|
209
|
+
|
210
|
+
# ========================================================================= #
|
211
|
+
# === target_for
|
212
|
+
# ========================================================================= #
|
213
|
+
def target_for(i)
|
214
|
+
_ = ''.dup
|
215
|
+
case i # case tag
|
216
|
+
# ======================================================================= #
|
217
|
+
# === :ensembl
|
218
|
+
# ======================================================================= #
|
219
|
+
when :ensembl
|
220
|
+
_ << '"https://www.ensembl.org/Human/Search/Results?q='
|
221
|
+
_ << @entry_ensembl.text+';name=Search;facet_species=Human"'
|
222
|
+
# ======================================================================= #
|
223
|
+
# === :dbget
|
224
|
+
# ======================================================================= #
|
225
|
+
when :dbget
|
226
|
+
_ << BASE_URL_FOR_DBGET
|
227
|
+
_ << @entry_dbget.text+'"'
|
228
|
+
# ======================================================================= #
|
229
|
+
# === :ncbi
|
230
|
+
# ======================================================================= #
|
231
|
+
when :ncbi
|
232
|
+
_ << BASE_URL_FOR_NCBI
|
233
|
+
_ << @entry_ncbi.text+'"'
|
234
|
+
end
|
235
|
+
return _
|
236
|
+
end
|
237
|
+
|
238
|
+
# ========================================================================= #
|
239
|
+
# === create_buttons (button tag, buttons tag)
|
240
|
+
# ========================================================================= #
|
241
|
+
def create_buttons
|
242
|
+
@button_quit = coloured_quit_button(colour: 'honeydew')
|
243
|
+
# ======================================================================= #
|
244
|
+
# === @button_search_dbget
|
245
|
+
# ======================================================================= #
|
246
|
+
@button_search_dbget = coloured_button('_DBGET_ivory')
|
247
|
+
@button_search_dbget.signal_connect(:clicked) { |w|
|
248
|
+
e rev+'Searching DBGET for: '+sfancy(@entry_dbget.text)
|
249
|
+
open_in_browser target_for(:dbget)
|
250
|
+
}
|
251
|
+
@button_search_dbget.fancy_tooltip = BASE_URL_FOR_DBGET.delete('"')
|
252
|
+
# ======================================================================= #
|
253
|
+
# === @button_ensembl
|
254
|
+
# ======================================================================= #
|
255
|
+
@button_ensembl = coloured_button('_Ensembl_lightblue')
|
256
|
+
@button_ensembl.signal_connect(:clicked) { |w|
|
257
|
+
e rev+'Searching ENSEMBL for: '+sfancy(@entry_ensembl.text)
|
258
|
+
open_in_browser target_for(:ensembl)
|
259
|
+
}
|
260
|
+
# ======================================================================= #
|
261
|
+
# === @button_search_ncbi
|
262
|
+
# ======================================================================= #
|
263
|
+
@button_search_ncbi = coloured_button('_NCBISearch_lightblue')
|
264
|
+
@button_search_ncbi.signal_connect(:clicked) { |w|
|
265
|
+
e rev+'Searching ncbi for: '+sfancy(@entry_ncbi.text)
|
266
|
+
open_in_browser target_for(:ncbi)
|
267
|
+
}
|
268
|
+
@button_search_ncbi.fancy_tooltip = BASE_URL_FOR_NCBI.delete('"')
|
269
|
+
# ======================================================================= #
|
270
|
+
# === @button_search_nih
|
271
|
+
# ======================================================================= #
|
272
|
+
@button_search_nih = coloured_button('_NIHSearch_lightblue')
|
273
|
+
@button_search_nih.signal_connect(:clicked) { |w|
|
274
|
+
e rev+'Searching NIH for: '+sfancy(@entry_nih.text)
|
275
|
+
target = '"https://search2.google.cit.nih.gov/search?'
|
276
|
+
target << 'client=NIH_frontend&site=NIH_Master&output=xml_no_dtd&'
|
277
|
+
target << 'proxystylesheet=NIH_frontend&ie=UTF-8&oe=UTF-8&filter=0&'
|
278
|
+
target << 'as_q='
|
279
|
+
tmp = @entry_nih.text.tr(' ','+')
|
280
|
+
target << tmp
|
281
|
+
target << '&'
|
282
|
+
target << 'num=40&btnG.x=29&btnG.y=10&btnG=Search&as_epq=&'
|
283
|
+
target << 'as_oq=&as_eq=&lr=&as_occt=any&as_dt=i&as_sitesearch=&sort='
|
284
|
+
target << '"'
|
285
|
+
}
|
286
|
+
end
|
287
|
+
|
288
|
+
# ========================================================================= #
|
289
|
+
# === focus_entry
|
290
|
+
#
|
291
|
+
# This helps you to focus an entry.
|
292
|
+
# ========================================================================= #
|
293
|
+
def focus_entry(which_entry)
|
294
|
+
case which_entry.to_s
|
295
|
+
when '1' then @entry_dbget.do_focus
|
296
|
+
when '2' then @entry_ncbi.do_focus
|
297
|
+
when '3' then @entry_nih.do_focus
|
298
|
+
when '4' then @entry_ensembl.do_focus
|
299
|
+
end
|
300
|
+
end
|
301
|
+
|
302
|
+
# ========================================================================= #
|
303
|
+
# === create_vbox
|
304
|
+
# ========================================================================= #
|
305
|
+
def create_vbox
|
306
|
+
@frame = gtk_frame
|
307
|
+
@frame.label_widget = modify_bold_label('Search for BioStuff: ','slateblue')
|
308
|
+
@v_box.minimal(@menu_bar,2)
|
309
|
+
@v_box.minimal(@entry_dbget,6)
|
310
|
+
@v_box.minimal(@button_search_dbget,6)
|
311
|
+
@v_box.minimal(@entry_ncbi,6)
|
312
|
+
@v_box.minimal(@button_search_ncbi,6)
|
313
|
+
@v_box.minimal(@entry_nih,6)
|
314
|
+
@v_box.minimal(@button_search_nih,6)
|
315
|
+
@v_box.minimal(@entry_ensembl,6)
|
316
|
+
@v_box.minimal(@button_ensembl,6)
|
317
|
+
@v_box.minimal(@checkbox_synchronize,6)
|
318
|
+
# The quit button can be found on the very bottom.
|
319
|
+
@v_box.maximal(@button_quit, 6)
|
320
|
+
@frame = gtk_frame(@v_box) # And this is the main frame.
|
321
|
+
end
|
322
|
+
|
323
|
+
# ========================================================================= #
|
324
|
+
# === favicon?
|
325
|
+
# ========================================================================= #
|
326
|
+
def favicon?
|
327
|
+
:tabble
|
328
|
+
end
|
329
|
+
|
330
|
+
# ========================================================================= #
|
331
|
+
# === connect_skeleton (connect tag)
|
332
|
+
# ========================================================================= #
|
333
|
+
def connect_skeleton
|
334
|
+
abort_on_exception
|
335
|
+
pack_start(@frame)
|
336
|
+
end
|
337
|
+
|
338
|
+
# ========================================================================= #
|
339
|
+
# === run (run tag)
|
340
|
+
# ========================================================================= #
|
341
|
+
def run
|
342
|
+
create_skeleton_then_connect_skeleton
|
343
|
+
end
|
344
|
+
|
345
|
+
# ========================================================================= #
|
346
|
+
# === Bioroebe::GUI::Gtk::WwwFinder.run
|
347
|
+
# ========================================================================= #
|
348
|
+
def self.run(
|
349
|
+
i = ARGV
|
350
|
+
)
|
351
|
+
require 'gtk_paradise/run'
|
352
|
+
_ = ::Bioroebe::GUI::Gtk::WwwFinder.new(i)
|
353
|
+
r = ::Gtk.run
|
354
|
+
r << _
|
355
|
+
r.add_shortcut(1, 'focus_entry(1)', :alt)
|
356
|
+
r.add_shortcut(2, 'focus_entry(2)', :alt)
|
357
|
+
r.add_shortcut(3, 'focus_entry(3)', :alt)
|
358
|
+
r.add_shortcut(4, 'focus_entry(4)', :alt)
|
359
|
+
r.background_colour :white
|
360
|
+
r.automatic_size_then_automatic_title
|
361
|
+
r.top_left_then_run
|
362
|
+
end; self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::WwwFinder.start_gui_application
|
363
|
+
|
364
|
+
end; end; end; end
|
365
|
+
|
366
|
+
if __FILE__ == $PROGRAM_NAME
|
367
|
+
Bioroebe::GUI::Gtk::WwwFinder.run
|
368
|
+
end
|