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
@@ -0,0 +1,119 @@
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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::ShowRestrictionEnzymes
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#
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# This class will show (thus, output) all available/registered
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# restriction enzymes.
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#
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#
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#
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# =========================================================================== #
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require 'bioroebe/base/base.rb'
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module Bioroebe
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class ShowRestrictionEnzymes < Base # === Bioroebe::ShowRestrictionEnzymes
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require 'bioroebe/enzymes/restriction_enzymes_file.rb'
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def initialize(
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)
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reset
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run if run_already
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end
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# ========================================================================= #
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# === reset
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# ========================================================================= #
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def reset
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super()
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# ======================================================================= #
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# === @use_colours
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# ======================================================================= #
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@use_colours = true
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end
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# ========================================================================= #
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# === notify_the_user_about_the_available_restriction_enzymes
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# ========================================================================= #
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def notify_the_user_about_the_available_restriction_enzymes
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erev 'Available Restriction Enzymes (from file '+
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sfile(::Bioroebe.restriction_enzymes_file)+'):'
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# ======================================================================= #
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# Obtain all restriction enzymes next, in Array form.
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# ======================================================================= #
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::Bioroebe.restriction_enzymes(:array_format).each {|key,value|
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}
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end
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# ========================================================================= #
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# === report_how_many_restriction_enzymes_were_found
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# ========================================================================= #
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def report_how_many_restriction_enzymes_were_found
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erev "A total of #{sfancy(n_enzymes)}#{rev} "\
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"registered restrictions-enzymes were found."
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end
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# ========================================================================= #
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# === colourize_value
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#
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# use of colours.
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# ========================================================================= #
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def colourize_value(i)
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if use_colours?
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i = slateblue(i)
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if i.include? ' ' # Here we also assume that this has at least one number.
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splitted = i.split ' '
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splitted[-1] = crimson(splitted[-1]) # Colourize the number red.
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i = splitted.join ' '
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end
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end
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i
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end
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# ========================================================================= #
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# === run (run tag)
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def run
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notify_the_user_about_the_available_restriction_enzymes
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report_how_many_restriction_enzymes_were_found
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end
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# ========================================================================= #
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# === Bioroebe::ShowRestrictionEnzymes[]
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# ========================================================================= #
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def self.[](i = '')
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new(i)
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end
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end
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# =========================================================================== #
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# === Bioroebe.show_restriction_enzymes
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#
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# Use this method if you wish to show all restriction enzymes.
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# =========================================================================== #
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def self.show_restriction_enzymes
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::Bioroebe::ShowRestrictionEnzymes.new # bl $BIOROEBE/show_restriction_enzymes.rb
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end
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end
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Bioroebe::ShowRestrictionEnzymes[]
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end # showrestrictionenzymes
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# =========================================================================== #
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# require 'bioroebe/exceptions/exceptions.rb'
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# =========================================================================== #
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module Bioroebe
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# === Declare the error for an invalid aminoacid.
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#
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# This will refer to the IUPAC code for aminoacids.
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# ========================================================================= #
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class InvalidAminoacid < StandardError # === Bioroebe::InvalidAminoacid
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end
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end
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This directory will contain C++ code that should eventually be usable
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to interact with the BioRoebe ruby code. It can, however had, also
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be used standalone, in some cases.
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Note that C and C++ are not as important as Java, though. Java will
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be the second supported language after Ruby, as far as the BioRoebe
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project is concerned.
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// Main.cpp
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using namespace std;
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/*
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* addition()
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|
+
*/
|
11
|
+
int addition(int a, int b)
|
12
|
+
{
|
13
|
+
int r;
|
14
|
+
r = a+b;
|
15
|
+
return r;
|
16
|
+
}
|
17
|
+
|
18
|
+
|
19
|
+
int main(int argc, char *argv[])
|
20
|
+
{
|
21
|
+
|
22
|
+
int z;
|
23
|
+
|
24
|
+
z = addition(5, 3);
|
25
|
+
|
26
|
+
cout << "The result is " << z << endl;
|
27
|
+
// TODO: delete the above
|
28
|
+
Sequence sequence_object("ATCGTTGC");
|
29
|
+
|
30
|
+
cout << sequence_object.query_sequence() << endl;
|
31
|
+
|
32
|
+
sequence_object.report_size();
|
33
|
+
sequence_object.report_type();
|
34
|
+
/* If we need to ask the user for a new sequence,
|
35
|
+
* enter here.
|
36
|
+
sequence_object.obtain_user_input();
|
37
|
+
*/
|
38
|
+
|
39
|
+
cout << sequence_object.query_sequence() << endl;
|
40
|
+
cout << "The length of this nucleotide sequence is: "
|
41
|
+
<< sequence_object.query_length() << endl;
|
42
|
+
|
43
|
+
return EXIT_SUCCESS; // Defined in the header <cstdlib>.
|
44
|
+
|
45
|
+
} // run main.cpp
|
@@ -0,0 +1,24 @@
|
|
1
|
+
/*
|
2
|
+
* This class shall store a single Nucleotide-sequence.
|
3
|
+
*/
|
4
|
+
#include <iostream>
|
5
|
+
|
6
|
+
using namespace std;
|
7
|
+
|
8
|
+
class Nucleotide {
|
9
|
+
|
10
|
+
private:
|
11
|
+
int length; /* The length of our Nucleotide String */
|
12
|
+
|
13
|
+
public:
|
14
|
+
Nucleotide (int,int);
|
15
|
+
Nucleotide::~Nucleotide();
|
16
|
+
int area() { return (width * height); }
|
17
|
+
|
18
|
+
/*
|
19
|
+
* report()
|
20
|
+
*/
|
21
|
+
void report() {
|
22
|
+
cout << "Our nucleotide has the following attributes:" << endl;
|
23
|
+
}
|
24
|
+
};
|
@@ -0,0 +1,348 @@
|
|
1
|
+
/*
|
2
|
+
* This file is a simple implementation for the nussinov-algorithm
|
3
|
+
* in C++.
|
4
|
+
*
|
5
|
+
* It uses the same GPLv2 licence as the rest of the Bioroebe project.
|
6
|
+
*/
|
7
|
+
|
8
|
+
#include <iostream>
|
9
|
+
#include <string>
|
10
|
+
#include <vector>
|
11
|
+
|
12
|
+
#define TITLE_FOR_THIS_FILE "Just another Nussinov Calculator:"
|
13
|
+
|
14
|
+
using namespace std;
|
15
|
+
|
16
|
+
int match(int i, int j, string &s)
|
17
|
+
{
|
18
|
+
/*
|
19
|
+
* Initialize the two Integers A and B.
|
20
|
+
*/
|
21
|
+
int A {static_cast<int>(s.at(i-1))},
|
22
|
+
B {static_cast<int>(s.at(j-1))};
|
23
|
+
|
24
|
+
switch (A-B) {
|
25
|
+
case 20:
|
26
|
+
case -20:
|
27
|
+
return 1;
|
28
|
+
break;
|
29
|
+
case -4:
|
30
|
+
case 4:
|
31
|
+
return 1;
|
32
|
+
break;
|
33
|
+
default:
|
34
|
+
return 0;
|
35
|
+
}
|
36
|
+
return 1;
|
37
|
+
}
|
38
|
+
|
39
|
+
class node
|
40
|
+
{
|
41
|
+
public:
|
42
|
+
vector<node*> branches;
|
43
|
+
char Base;
|
44
|
+
|
45
|
+
node();
|
46
|
+
node(char);
|
47
|
+
node* addchild(node&);
|
48
|
+
node* addparent(node&);
|
49
|
+
|
50
|
+
void print();
|
51
|
+
};
|
52
|
+
|
53
|
+
node::node(): Base {'0'} {}
|
54
|
+
node::node(char c): Base{c} {}
|
55
|
+
|
56
|
+
node* node::addchild(node& leaf) {
|
57
|
+
branches.push_back(&leaf);
|
58
|
+
return this;
|
59
|
+
}
|
60
|
+
|
61
|
+
node* node::addparent(node& stem) {
|
62
|
+
// branch.branches.clear();
|
63
|
+
stem.addchild(*this);
|
64
|
+
return this;
|
65
|
+
}
|
66
|
+
|
67
|
+
/*
|
68
|
+
* node::print()
|
69
|
+
*/
|
70
|
+
void node::print()
|
71
|
+
{
|
72
|
+
if (branches.size() > 0)
|
73
|
+
{
|
74
|
+
for (auto& b: branches)
|
75
|
+
{
|
76
|
+
b->print();
|
77
|
+
}
|
78
|
+
} else {
|
79
|
+
if (Base != '0')
|
80
|
+
{
|
81
|
+
cout << Base;
|
82
|
+
cout << endl;
|
83
|
+
}
|
84
|
+
}
|
85
|
+
return;
|
86
|
+
}
|
87
|
+
|
88
|
+
class N {
|
89
|
+
public:
|
90
|
+
vector<vector<N*>> trace;
|
91
|
+
int value;
|
92
|
+
int i, j;
|
93
|
+
int calculate(string &s, vector<vector<N>> &NA);
|
94
|
+
|
95
|
+
void set(int v);
|
96
|
+
N(int i, int j);
|
97
|
+
|
98
|
+
vector<string> addtrackback(string &s);
|
99
|
+
int numberofbranches();
|
100
|
+
};
|
101
|
+
|
102
|
+
N::N(int i, int j): value {0}, i{i}, j{j} {}
|
103
|
+
void N::set(int v) {value = v; return; }
|
104
|
+
|
105
|
+
int N::numberofbranches()
|
106
|
+
{
|
107
|
+
int branches = 0;
|
108
|
+
if (trace.size() == 0) { return 0; }
|
109
|
+
for (auto& t: trace)
|
110
|
+
{
|
111
|
+
branches++;
|
112
|
+
for (auto& b: t)
|
113
|
+
{
|
114
|
+
branches += b->numberofbranches();
|
115
|
+
}
|
116
|
+
}
|
117
|
+
branches--;
|
118
|
+
return branches;
|
119
|
+
}
|
120
|
+
|
121
|
+
vector<string> N::addtrackback(string &s)
|
122
|
+
{
|
123
|
+
vector<string> retval;
|
124
|
+
if (trace.size() == 0)
|
125
|
+
{
|
126
|
+
string container = "";
|
127
|
+
for (int loopctr = i; loopctr <= j; loopctr++)
|
128
|
+
{
|
129
|
+
container = container + '.';
|
130
|
+
}
|
131
|
+
retval.push_back(container+s);
|
132
|
+
}
|
133
|
+
for (auto &t: trace)
|
134
|
+
{
|
135
|
+
if (t.size() == 1)
|
136
|
+
{
|
137
|
+
if (t.front()->i == i+1)
|
138
|
+
{
|
139
|
+
string base = ")" + s;
|
140
|
+
for (auto m: t.front()->addtrackback(base))
|
141
|
+
{
|
142
|
+
retval.push_back("(" + m);
|
143
|
+
}
|
144
|
+
} else {
|
145
|
+
string base = "." + s;
|
146
|
+
for (auto b: t.front()->addtrackback(base))
|
147
|
+
{
|
148
|
+
retval.push_back(b);
|
149
|
+
}
|
150
|
+
}
|
151
|
+
} else {
|
152
|
+
string base = ")" + s;
|
153
|
+
for (auto lb: t.back()->addtrackback(base))
|
154
|
+
{
|
155
|
+
string rbase = "(" + lb;
|
156
|
+
for (auto lb: t.front()->addtrackback(rbase))
|
157
|
+
{
|
158
|
+
retval.push_back(lb);
|
159
|
+
}
|
160
|
+
}
|
161
|
+
|
162
|
+
}
|
163
|
+
}
|
164
|
+
return retval;
|
165
|
+
}
|
166
|
+
|
167
|
+
/*
|
168
|
+
* printtrackbacks()
|
169
|
+
*/
|
170
|
+
void printtrackbacks(N &Cell, string &s)
|
171
|
+
{
|
172
|
+
cout << endl;
|
173
|
+
for (unsigned int i = 1; i <= s.length(); i++)
|
174
|
+
{
|
175
|
+
cout << (i%10);
|
176
|
+
}
|
177
|
+
cout << endl;
|
178
|
+
for (unsigned int i = 1; i <= s.length(); i++)
|
179
|
+
{
|
180
|
+
cout << s.at(i-1);
|
181
|
+
}
|
182
|
+
cout << endl;
|
183
|
+
string startseq = "";
|
184
|
+
for (auto &seq: Cell.addtrackback(startseq))
|
185
|
+
{
|
186
|
+
cout << seq << endl;
|
187
|
+
}
|
188
|
+
return;
|
189
|
+
}
|
190
|
+
|
191
|
+
int N::calculate(string &s, vector<vector<N>> &NA)
|
192
|
+
{
|
193
|
+
int retval {0};
|
194
|
+
|
195
|
+
if ( (i >= j) || (i == (j-1)) )
|
196
|
+
{
|
197
|
+
value = 0;
|
198
|
+
return 0;
|
199
|
+
} else {
|
200
|
+
int candidate {0};
|
201
|
+
candidate = NA.at((i)-1).at((j-1)-1).value;
|
202
|
+
// not a match. cout << "N:" << candidate << " from i:" << i << " j:" << j << endl;
|
203
|
+
trace.push_back(vector<N*> {&NA.at((i)-1).at((j-1)-1)});
|
204
|
+
retval = candidate;
|
205
|
+
if (match((i), (j), s))
|
206
|
+
{
|
207
|
+
candidate = NA.at((i+1)-1).at((j-1)-1).value + 1;
|
208
|
+
// branchless match between the outermose bases. cout << "M:" << candidate << " from i:" << i+1 << " j:" << j-1 << endl;
|
209
|
+
if (candidate >= retval)
|
210
|
+
{
|
211
|
+
if (candidate > retval)
|
212
|
+
{
|
213
|
+
trace.clear();
|
214
|
+
retval = candidate;
|
215
|
+
}
|
216
|
+
trace.push_back(vector<N*> {/*&NA.at((i)-1).at((i)-1),*/ &NA.at((i+1)-1).at((j-1)-1)});
|
217
|
+
}
|
218
|
+
}
|
219
|
+
for (int k = (i+1); k < (j-1); k++)
|
220
|
+
{
|
221
|
+
if (match(k, j, s))
|
222
|
+
{
|
223
|
+
candidate = NA.at((i)-1).at((k-1)-1).value + NA.at((k+1)-1).at((j-1)-1).value + 1;
|
224
|
+
// branching match cout << "B:" << candidate << " from i:" << i+1 << " j:" << j-1 << endl;
|
225
|
+
if (candidate >= retval)
|
226
|
+
{
|
227
|
+
if (candidate > retval)
|
228
|
+
{
|
229
|
+
trace.clear();
|
230
|
+
retval = candidate;
|
231
|
+
}
|
232
|
+
trace.push_back(vector<N*> {&NA.at((i)-1).at((k-1)-1), &NA.at((k+1)-1).at((j-1)-1)});
|
233
|
+
}
|
234
|
+
}
|
235
|
+
}
|
236
|
+
}
|
237
|
+
value = retval;
|
238
|
+
return retval;
|
239
|
+
}
|
240
|
+
|
241
|
+
/*
|
242
|
+
* print_the_matrix()
|
243
|
+
*
|
244
|
+
* Used to print out our matrix.
|
245
|
+
*/
|
246
|
+
void print_the_matrix(vector<vector<N>> &NA, string &s)
|
247
|
+
{
|
248
|
+
cout << endl;
|
249
|
+
cout << '\t' << '\t' << 1;
|
250
|
+
for (size_t i = 1; i < s.size(); i++ )
|
251
|
+
{
|
252
|
+
cout << '\t' << i+1;
|
253
|
+
}
|
254
|
+
cout << endl;
|
255
|
+
cout << '\t' << '\t' << s.at(0);
|
256
|
+
for (size_t i = 1; i < s.size(); i++ )
|
257
|
+
{
|
258
|
+
cout << '\t' << s.at(i);
|
259
|
+
}
|
260
|
+
cout << endl;
|
261
|
+
for (size_t i = 0; i < s.size(); i++ )
|
262
|
+
{
|
263
|
+
cout << i+1 << '\t' << s.at(i);
|
264
|
+
for (size_t j = 0; j < s.size(); j++)
|
265
|
+
{
|
266
|
+
cout << '\t' << NA.at(i).at(j).value;
|
267
|
+
}
|
268
|
+
cout << endl;
|
269
|
+
}
|
270
|
+
return;
|
271
|
+
}
|
272
|
+
|
273
|
+
/*
|
274
|
+
* traceback()
|
275
|
+
*
|
276
|
+
* Should not be necessary.
|
277
|
+
*
|
278
|
+
*/
|
279
|
+
/*void traceback(vector<vector<N>> &NA, string &s, node &n)
|
280
|
+
{ return; }
|
281
|
+
*/
|
282
|
+
|
283
|
+
/*
|
284
|
+
* The nussinov algorithm.
|
285
|
+
*/
|
286
|
+
void nussinov_algorithm(string &s)
|
287
|
+
{
|
288
|
+
// Create our vector-field datastructure first.
|
289
|
+
vector<vector<N>> NA;
|
290
|
+
|
291
|
+
for (size_t i = 0; i < s.length(); i++)
|
292
|
+
{
|
293
|
+
vector<N> NRow;
|
294
|
+
for (size_t j = 0; j < s.length(); j++)
|
295
|
+
{
|
296
|
+
NRow.push_back(N(i+1, j+1));
|
297
|
+
}
|
298
|
+
NA.push_back(NRow);
|
299
|
+
}
|
300
|
+
|
301
|
+
// fill in from first off-diagonal to the very end
|
302
|
+
for (int a = -1; a < static_cast<int>(s.length()); a++)
|
303
|
+
{
|
304
|
+
for (int b {0}, c {a}; (b < static_cast<int>(s.length()) && c < static_cast<int>(s.length())); b++, c++)
|
305
|
+
{
|
306
|
+
if (c < 0)
|
307
|
+
{
|
308
|
+
continue;
|
309
|
+
} else {
|
310
|
+
NA.at(b).at(c).calculate(s, NA);
|
311
|
+
}
|
312
|
+
}
|
313
|
+
}
|
314
|
+
// print the matrix
|
315
|
+
print_the_matrix(NA, s);
|
316
|
+
|
317
|
+
// Print out the different candidate pairings.
|
318
|
+
cout << endl << "Number of Seuqence Candidates: "
|
319
|
+
<< NA.at((1)-1).at(s.length()-1).numberofbranches()+1 << endl;
|
320
|
+
|
321
|
+
// Show the trace back.
|
322
|
+
printtrackbacks(NA.at((1)-1).at(s.length()-1), s);
|
323
|
+
|
324
|
+
// traceback(NA, s, n);
|
325
|
+
return;
|
326
|
+
}
|
327
|
+
|
328
|
+
int main(int argc, char* argv[]) {
|
329
|
+
|
330
|
+
string s {""};
|
331
|
+
|
332
|
+
if (argc > 1)
|
333
|
+
{
|
334
|
+
string s = argv[1];
|
335
|
+
} else {
|
336
|
+
cout << TITLE_FOR_THIS_FILE << endl << endl;
|
337
|
+
cout << "Invoke this class either with a Sequence as "\
|
338
|
+
"First Parameter - or Enter Sequence Below." << endl << endl;
|
339
|
+
cout << "For Best Experience, Display (or Pipe) the Output in 'less -x4'." << endl << endl;
|
340
|
+
cout << "Refer to R.Nussinov, G.Pieczenik, J.R. Griggs, and D.J.Kleitman" << endl;
|
341
|
+
cout << "SIAM Journal on Applied Mathematics, 1978(35), 68-82" << endl << endl;
|
342
|
+
cout << "Enter Sequence next: ";
|
343
|
+
/* Get the user input next */
|
344
|
+
cin >> s;
|
345
|
+
}
|
346
|
+
nussinov_algorithm(s);
|
347
|
+
return 0;
|
348
|
+
} // run nussinov_algorithm.cpp SAVE_AS_IS
|
Binary file
|