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
data/doc/setup.rb
ADDED
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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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# === setup.rb
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#
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# Copyright (c) 2000-2005 Minero Aoki
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#
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# This program is free software.
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#
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# You can distribute/modify this program under the terms of
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# the GNU LGPL, Lesser General Public License version 2.1.
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#
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# Note that this was modified in 2021 - a few begin/rescue clauses
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# were added.
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# =========================================================================== #
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unless Errno.const_defined?(:ENOTEMPTY) # Windows?
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module Errno
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class ENOTEMPTY
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# We do not raise this exception, implementation is not needed.
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end
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end
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end
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def File.binread(fname)
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open(fname, 'rb') {|f|
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return f.read
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}
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end
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# for corrupted Windows' stat(2)
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def File.dir?(path)
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File.directory?((path[-1,1] == '/') ? path : path + '/')
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end
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class ConfigTable
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include Enumerable
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# ========================================================================= #
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# === initialize
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# ========================================================================= #
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def initialize(rbconfig)
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@rbconfig = rbconfig
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@items = []
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@table = {}
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# options
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@install_prefix = nil
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@config_opt = nil
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@verbose = true
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@no_harm = false
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end
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attr_accessor :install_prefix
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attr_accessor :config_opt
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attr_writer :no_harm
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attr_writer :verbose
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# ========================================================================= #
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# === verbose?
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# ========================================================================= #
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def verbose?
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@verbose
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end
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# ========================================================================= #
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# === no_harm?
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# ========================================================================= #
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def no_harm?
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@no_harm
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end
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# ========================================================================= #
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# === []
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# ========================================================================= #
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def [](key)
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lookup(key).resolve(self)
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end
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def []=(key, val)
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lookup(key).set val
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end
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# ========================================================================= #
|
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+
# === names
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# ========================================================================= #
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def names
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@items.map {|i| i.name }
|
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+
end
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|
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def each(&block)
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@items.each(&block)
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+
end
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+
|
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# === key?
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def key?(i)
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@table.key?(i)
|
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+
end
|
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+
|
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# ========================================================================= #
|
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+
# === lookup
|
103
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+
# ========================================================================= #
|
104
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+
def lookup(name)
|
105
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+
@table[name] or setup_rb_error "no such config item: #{name}"
|
106
|
+
end
|
107
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+
|
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# ========================================================================= #
|
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# === add
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# ========================================================================= #
|
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+
def add(item)
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@items.push item
|
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@table[item.name] = item
|
114
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end
|
115
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+
|
116
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# ========================================================================= #
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117
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+
# === remove
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# ========================================================================= #
|
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def remove(name)
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item = lookup(name)
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@items.delete_if {|i| i.name == name }
|
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@table.delete_if {|inner_name, i| i.name == inner_name }
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item
|
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end
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+
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126
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# ========================================================================= #
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# === load_script
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# ========================================================================= #
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def load_script(path, inst = nil)
|
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+
if File.file?(path)
|
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MetaConfigEnvironment.new(self, inst).instance_eval File.read(path), path
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end
|
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+
end
|
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+
|
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# ========================================================================= #
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# === savefile
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# ========================================================================= #
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def savefile
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'.config'
|
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end
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# ========================================================================= #
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# === load_savefile
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# ========================================================================= #
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def load_savefile
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begin
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File.foreach(savefile()) { |line|
|
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k, v = *line.split(/=/, 2)
|
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self[k] = v.strip
|
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}
|
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rescue Errno::ENOENT
|
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setup_rb_error $!.message + "\n#{File.basename($0)} config first"
|
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end
|
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end
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# ========================================================================= #
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# === save
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# ========================================================================= #
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def save
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@items.each {|i| i.value }
|
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File.open(savefile(), 'w') {|f|
|
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@items.each do |i|
|
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f.printf "%s=%s\n", i.name, i.value if i.value? and i.value
|
164
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+
end
|
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}
|
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+
end
|
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+
|
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# ========================================================================= #
|
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# === load_standard_entries
|
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|
+
# ========================================================================= #
|
171
|
+
def load_standard_entries
|
172
|
+
standard_entries(@rbconfig).each {|entry|
|
173
|
+
add entry
|
174
|
+
}
|
175
|
+
end
|
176
|
+
|
177
|
+
# ========================================================================= #
|
178
|
+
# === standard_entries
|
179
|
+
# ========================================================================= #
|
180
|
+
def standard_entries(rbconfig)
|
181
|
+
c = rbconfig
|
182
|
+
|
183
|
+
rubypath = File.join(c['bindir'], c['ruby_install_name'] + c['EXEEXT'])
|
184
|
+
|
185
|
+
major = c['MAJOR'].to_i
|
186
|
+
minor = c['MINOR'].to_i
|
187
|
+
teeny = c['TEENY'].to_i
|
188
|
+
version = "#{major}.#{minor}"
|
189
|
+
|
190
|
+
# ======================================================================= #
|
191
|
+
# ruby ver. >= 1.4.4?
|
192
|
+
# ======================================================================== #
|
193
|
+
newpath_p = ((major >= 2) or
|
194
|
+
((major == 1) and
|
195
|
+
((minor >= 5) or
|
196
|
+
((minor == 4) and (teeny >= 4)))))
|
197
|
+
|
198
|
+
if c['rubylibdir']
|
199
|
+
# V > 1.6.3
|
200
|
+
libruby = "#{c['prefix']}/lib/ruby"
|
201
|
+
librubyver = c['rubylibdir']
|
202
|
+
librubyverarch = c['archdir']
|
203
|
+
siteruby = c['sitedir']
|
204
|
+
siterubyver = c['sitelibdir']
|
205
|
+
siterubyverarch = c['sitearchdir']
|
206
|
+
elsif newpath_p
|
207
|
+
# 1.4.4 <= V <= 1.6.3
|
208
|
+
libruby = "#{c['prefix']}/lib/ruby"
|
209
|
+
librubyver = "#{c['prefix']}/lib/ruby/#{version}"
|
210
|
+
librubyverarch = "#{c['prefix']}/lib/ruby/#{version}/#{c['arch']}"
|
211
|
+
siteruby = c['sitedir']
|
212
|
+
siterubyver = "$siteruby/#{version}"
|
213
|
+
siterubyverarch = "$siterubyver/#{c['arch']}"
|
214
|
+
else
|
215
|
+
# V < 1.4.4
|
216
|
+
libruby = "#{c['prefix']}/lib/ruby"
|
217
|
+
librubyver = "#{c['prefix']}/lib/ruby/#{version}"
|
218
|
+
librubyverarch = "#{c['prefix']}/lib/ruby/#{version}/#{c['arch']}"
|
219
|
+
siteruby = "#{c['prefix']}/lib/ruby/#{version}/site_ruby"
|
220
|
+
siterubyver = siteruby
|
221
|
+
siterubyverarch = "$siterubyver/#{c['arch']}"
|
222
|
+
end
|
223
|
+
parameterize = lambda {|path|
|
224
|
+
path.sub(/\A#{Regexp.quote(c['prefix'])}/, '$prefix')
|
225
|
+
}
|
226
|
+
|
227
|
+
if arg = c['configure_args'].split.detect {|inner_arg| /--with-make-prog=/ =~ inner_arg }
|
228
|
+
makeprog = arg.sub(/'/, '').split(/=/, 2)[1]
|
229
|
+
else
|
230
|
+
makeprog = 'make'
|
231
|
+
end
|
232
|
+
|
233
|
+
[
|
234
|
+
ExecItem.new('installdirs', 'std/site/home',
|
235
|
+
'std: install under libruby; site: install under site_ruby; home: install under $HOME')\
|
236
|
+
{|val, table|
|
237
|
+
case val
|
238
|
+
when 'std'
|
239
|
+
table['rbdir'] = '$librubyver'
|
240
|
+
table['sodir'] = '$librubyverarch'
|
241
|
+
when 'site'
|
242
|
+
table['rbdir'] = '$siterubyver'
|
243
|
+
table['sodir'] = '$siterubyverarch'
|
244
|
+
when 'home'
|
245
|
+
setup_rb_error '$HOME was not set' unless ENV['HOME']
|
246
|
+
table['prefix'] = ENV['HOME']
|
247
|
+
table['rbdir'] = '$libdir/ruby'
|
248
|
+
table['sodir'] = '$libdir/ruby'
|
249
|
+
end
|
250
|
+
},
|
251
|
+
PathItem.new('prefix', 'path', c['prefix'],
|
252
|
+
'path prefix of target environment'),
|
253
|
+
PathItem.new('bindir', 'path', parameterize.call(c['bindir']),
|
254
|
+
'the directory for commands'),
|
255
|
+
PathItem.new('libdir', 'path', parameterize.call(c['libdir']),
|
256
|
+
'the directory for libraries'),
|
257
|
+
PathItem.new('datadir', 'path', parameterize.call(c['datadir']),
|
258
|
+
'the directory for shared data'),
|
259
|
+
PathItem.new('mandir', 'path', parameterize.call(c['mandir']),
|
260
|
+
'the directory for man pages'),
|
261
|
+
PathItem.new('sysconfdir', 'path', parameterize.call(c['sysconfdir']),
|
262
|
+
'the directory for system configuration files'),
|
263
|
+
PathItem.new('localstatedir', 'path', parameterize.call(c['localstatedir']),
|
264
|
+
'the directory for local state data'),
|
265
|
+
PathItem.new('libruby', 'path', libruby,
|
266
|
+
'the directory for ruby libraries'),
|
267
|
+
PathItem.new('librubyver', 'path', librubyver,
|
268
|
+
'the directory for standard ruby libraries'),
|
269
|
+
PathItem.new('librubyverarch', 'path', librubyverarch,
|
270
|
+
'the directory for standard ruby extensions'),
|
271
|
+
PathItem.new('siteruby', 'path', siteruby,
|
272
|
+
'the directory for version-independent aux ruby libraries'),
|
273
|
+
PathItem.new('siterubyver', 'path', siterubyver,
|
274
|
+
'the directory for aux ruby libraries'),
|
275
|
+
PathItem.new('siterubyverarch', 'path', siterubyverarch,
|
276
|
+
'the directory for aux ruby binaries'),
|
277
|
+
PathItem.new('rbdir', 'path', '$siterubyver',
|
278
|
+
'the directory for ruby scripts'),
|
279
|
+
PathItem.new('sodir', 'path', '$siterubyverarch',
|
280
|
+
'the directory for ruby extentions'),
|
281
|
+
PathItem.new('rubypath', 'path', rubypath,
|
282
|
+
'the path to set to #! line'),
|
283
|
+
ProgramItem.new('rubyprog', 'name', rubypath,
|
284
|
+
'the ruby program using for installation'),
|
285
|
+
ProgramItem.new('makeprog', 'name', makeprog,
|
286
|
+
'the make program to compile ruby extentions'),
|
287
|
+
SelectItem.new('shebang', 'all/ruby/never', 'ruby',
|
288
|
+
'shebang line (#!) editing mode'),
|
289
|
+
BoolItem.new('without-ext', 'yes/no', 'no',
|
290
|
+
'does not compile/install ruby extentions')
|
291
|
+
]
|
292
|
+
end
|
293
|
+
private :standard_entries
|
294
|
+
|
295
|
+
# ========================================================================= #
|
296
|
+
# === load_multipackage_entries
|
297
|
+
# ========================================================================= #
|
298
|
+
def load_multipackage_entries
|
299
|
+
multipackage_entries().each do |ent|
|
300
|
+
add ent
|
301
|
+
end
|
302
|
+
end
|
303
|
+
|
304
|
+
# ========================================================================= #
|
305
|
+
# === multipackage_entries
|
306
|
+
# ========================================================================= #
|
307
|
+
def multipackage_entries
|
308
|
+
[
|
309
|
+
PackageSelectionItem.new('with', 'name,name...', '', 'ALL',
|
310
|
+
'package names that you want to install'),
|
311
|
+
PackageSelectionItem.new('without', 'name,name...', '', 'NONE',
|
312
|
+
'package names that you do not want to install')
|
313
|
+
]
|
314
|
+
end
|
315
|
+
private :multipackage_entries
|
316
|
+
|
317
|
+
ALIASES = {
|
318
|
+
'std-ruby' => 'librubyver',
|
319
|
+
'stdruby' => 'librubyver',
|
320
|
+
'rubylibdir' => 'librubyver',
|
321
|
+
'archdir' => 'librubyverarch',
|
322
|
+
'site-ruby-common' => 'siteruby', # For backward compatibility
|
323
|
+
'site-ruby' => 'siterubyver', # For backward compatibility
|
324
|
+
'bin-dir' => 'bindir',
|
325
|
+
'rb-dir' => 'rbdir',
|
326
|
+
'so-dir' => 'sodir',
|
327
|
+
'data-dir' => 'datadir',
|
328
|
+
'ruby-path' => 'rubypath',
|
329
|
+
'ruby-prog' => 'rubyprog',
|
330
|
+
'ruby' => 'rubyprog',
|
331
|
+
'make-prog' => 'makeprog',
|
332
|
+
'make' => 'makeprog'
|
333
|
+
}
|
334
|
+
|
335
|
+
# ========================================================================= #
|
336
|
+
# === fixup
|
337
|
+
# ========================================================================= #
|
338
|
+
def fixup
|
339
|
+
ALIASES.each { |ali, name|
|
340
|
+
@table[ali] = @table[name]
|
341
|
+
}
|
342
|
+
@items.freeze
|
343
|
+
@table.freeze
|
344
|
+
@options_re = /\A--(#{@table.keys.join('|')})(?:=(.*))?\z/
|
345
|
+
end
|
346
|
+
|
347
|
+
# ========================================================================= #
|
348
|
+
# === parse_opt
|
349
|
+
# ========================================================================= #
|
350
|
+
def parse_opt(opt)
|
351
|
+
m = @options_re.match(opt) or setup_rb_error "config: unknown option #{opt}"
|
352
|
+
m.to_a[1,2]
|
353
|
+
end
|
354
|
+
|
355
|
+
def dllext
|
356
|
+
@rbconfig['DLEXT']
|
357
|
+
end
|
358
|
+
|
359
|
+
def value_config?(name)
|
360
|
+
lookup(name).value?
|
361
|
+
end
|
362
|
+
|
363
|
+
class Item
|
364
|
+
def initialize(name, template, default, desc)
|
365
|
+
@name = name.freeze
|
366
|
+
@template = template
|
367
|
+
@value = default
|
368
|
+
@default = default
|
369
|
+
@description = desc
|
370
|
+
end
|
371
|
+
|
372
|
+
attr_reader :name
|
373
|
+
attr_reader :description
|
374
|
+
|
375
|
+
attr_accessor :default
|
376
|
+
alias help_default default
|
377
|
+
|
378
|
+
def help_opt
|
379
|
+
"--#{@name}=#{@template}"
|
380
|
+
end
|
381
|
+
|
382
|
+
def value?
|
383
|
+
true
|
384
|
+
end
|
385
|
+
|
386
|
+
def value
|
387
|
+
@value
|
388
|
+
end
|
389
|
+
|
390
|
+
def resolve(table)
|
391
|
+
@value.gsub(%r<\$([^/]+)>) { table[$1] }
|
392
|
+
end
|
393
|
+
|
394
|
+
def set(val)
|
395
|
+
@value = check(val)
|
396
|
+
end
|
397
|
+
|
398
|
+
private
|
399
|
+
|
400
|
+
def check(val)
|
401
|
+
setup_rb_error "config: --#{name} requires argument" unless val
|
402
|
+
val
|
403
|
+
end
|
404
|
+
end
|
405
|
+
|
406
|
+
class BoolItem < Item
|
407
|
+
def config_type
|
408
|
+
'bool'
|
409
|
+
end
|
410
|
+
|
411
|
+
def help_opt
|
412
|
+
"--#{@name}"
|
413
|
+
end
|
414
|
+
|
415
|
+
private
|
416
|
+
|
417
|
+
def check(val)
|
418
|
+
return 'yes' unless val
|
419
|
+
case val
|
420
|
+
when /\Ay(es)?\z/i, /\At(rue)?\z/i then 'yes'
|
421
|
+
when /\An(o)?\z/i, /\Af(alse)\z/i then 'no'
|
422
|
+
else
|
423
|
+
setup_rb_error "config: --#{@name} accepts only yes/no for argument"
|
424
|
+
end
|
425
|
+
end
|
426
|
+
end
|
427
|
+
|
428
|
+
class PathItem < Item
|
429
|
+
def config_type
|
430
|
+
'path'
|
431
|
+
end
|
432
|
+
|
433
|
+
private
|
434
|
+
|
435
|
+
def check(path)
|
436
|
+
setup_rb_error "config: --#{@name} requires argument" unless path
|
437
|
+
path[0,1] == '$' ? path : File.expand_path(path)
|
438
|
+
end
|
439
|
+
end
|
440
|
+
|
441
|
+
class ProgramItem < Item
|
442
|
+
def config_type
|
443
|
+
'program'
|
444
|
+
end
|
445
|
+
end
|
446
|
+
|
447
|
+
class SelectItem < Item
|
448
|
+
def initialize(name, selection, default, desc)
|
449
|
+
super
|
450
|
+
@ok = selection.split('/')
|
451
|
+
end
|
452
|
+
|
453
|
+
def config_type
|
454
|
+
'select'
|
455
|
+
end
|
456
|
+
|
457
|
+
private
|
458
|
+
|
459
|
+
def check(val)
|
460
|
+
unless @ok.include?(val.strip)
|
461
|
+
setup_rb_error "config: use --#{@name}=#{@template} (#{val})"
|
462
|
+
end
|
463
|
+
val.strip
|
464
|
+
end
|
465
|
+
end
|
466
|
+
|
467
|
+
class ExecItem < Item
|
468
|
+
def initialize(name, selection, desc, &block)
|
469
|
+
super name, selection, nil, desc
|
470
|
+
@ok = selection.split('/')
|
471
|
+
@action = block
|
472
|
+
end
|
473
|
+
|
474
|
+
def config_type
|
475
|
+
'exec'
|
476
|
+
end
|
477
|
+
|
478
|
+
def value?
|
479
|
+
false
|
480
|
+
end
|
481
|
+
|
482
|
+
def resolve(table)
|
483
|
+
setup_rb_error "$#{name()} wrongly used as option value"
|
484
|
+
end
|
485
|
+
|
486
|
+
undef set
|
487
|
+
|
488
|
+
def evaluate(val, table)
|
489
|
+
v = val.strip.downcase
|
490
|
+
unless @ok.include?(v)
|
491
|
+
setup_rb_error "invalid option --#{@name}=#{val} (use #{@template})"
|
492
|
+
end
|
493
|
+
@action.call v, table
|
494
|
+
end
|
495
|
+
end
|
496
|
+
|
497
|
+
class PackageSelectionItem < Item
|
498
|
+
def initialize(name, template, default, help_default, desc)
|
499
|
+
super name, template, default, desc
|
500
|
+
@help_default = help_default
|
501
|
+
end
|
502
|
+
|
503
|
+
attr_reader :help_default
|
504
|
+
|
505
|
+
def config_type
|
506
|
+
'package'
|
507
|
+
end
|
508
|
+
|
509
|
+
private
|
510
|
+
|
511
|
+
def check(val)
|
512
|
+
unless File.dir?("packages/#{val}")
|
513
|
+
setup_rb_error "config: no such package: #{val}"
|
514
|
+
end
|
515
|
+
val
|
516
|
+
end
|
517
|
+
end
|
518
|
+
|
519
|
+
class MetaConfigEnvironment
|
520
|
+
def initialize(config, installer)
|
521
|
+
@config = config
|
522
|
+
@installer = installer
|
523
|
+
end
|
524
|
+
|
525
|
+
def config_names
|
526
|
+
@config.names
|
527
|
+
end
|
528
|
+
|
529
|
+
def config?(name)
|
530
|
+
@config.key?(name)
|
531
|
+
end
|
532
|
+
|
533
|
+
def bool_config?(name)
|
534
|
+
@config.lookup(name).config_type == 'bool'
|
535
|
+
end
|
536
|
+
|
537
|
+
def path_config?(name)
|
538
|
+
@config.lookup(name).config_type == 'path'
|
539
|
+
end
|
540
|
+
|
541
|
+
def value_config?(name)
|
542
|
+
@config.lookup(name).config_type != 'exec'
|
543
|
+
end
|
544
|
+
|
545
|
+
def add_config(item)
|
546
|
+
@config.add item
|
547
|
+
end
|
548
|
+
|
549
|
+
def add_bool_config(name, default, desc)
|
550
|
+
@config.add BoolItem.new(name, 'yes/no', default ? 'yes' : 'no', desc)
|
551
|
+
end
|
552
|
+
|
553
|
+
def add_path_config(name, default, desc)
|
554
|
+
@config.add PathItem.new(name, 'path', default, desc)
|
555
|
+
end
|
556
|
+
|
557
|
+
def set_config_default(name, default)
|
558
|
+
@config.lookup(name).default = default
|
559
|
+
end
|
560
|
+
|
561
|
+
def remove_config(name)
|
562
|
+
@config.remove(name)
|
563
|
+
end
|
564
|
+
|
565
|
+
# For only multipackage
|
566
|
+
def packages
|
567
|
+
raise '[setup.rb fatal] multi-package metaconfig API packages() called for single-package; contact application package vendor' unless @installer
|
568
|
+
@installer.packages
|
569
|
+
end
|
570
|
+
|
571
|
+
# For only multipackage
|
572
|
+
def declare_packages(list)
|
573
|
+
raise '[setup.rb fatal] multi-package metaconfig API declare_packages() called for single-package; contact application package vendor' unless @installer
|
574
|
+
@installer.packages = list
|
575
|
+
end
|
576
|
+
end
|
577
|
+
|
578
|
+
end # class ConfigTable
|
579
|
+
|
580
|
+
# This module requires: #verbose?, #no_harm?
|
581
|
+
module FileOperations
|
582
|
+
|
583
|
+
def mkdir_p(dirname, prefix = nil)
|
584
|
+
dirname = prefix + File.expand_path(dirname) if prefix
|
585
|
+
$stderr.puts "mkdir -p #{dirname}" if verbose?
|
586
|
+
return if no_harm?
|
587
|
+
|
588
|
+
# Does not check '/', it's too abnormal.
|
589
|
+
dirs = File.expand_path(dirname).split(%r<(?=/)>)
|
590
|
+
if /\A[a-z]:\z/i =~ dirs[0]
|
591
|
+
disk = dirs.shift
|
592
|
+
dirs[0] = disk + dirs[0]
|
593
|
+
end
|
594
|
+
dirs.each_index do |idx|
|
595
|
+
path = dirs[0..idx].join('')
|
596
|
+
Dir.mkdir path unless File.dir?(path)
|
597
|
+
end
|
598
|
+
end
|
599
|
+
|
600
|
+
def rm_f(path)
|
601
|
+
$stderr.puts "rm -f #{path}" if verbose?
|
602
|
+
return if no_harm?
|
603
|
+
force_remove_file path
|
604
|
+
end
|
605
|
+
|
606
|
+
def rm_rf(path)
|
607
|
+
$stderr.puts "rm -rf #{path}" if verbose?
|
608
|
+
return if no_harm?
|
609
|
+
remove_tree path
|
610
|
+
end
|
611
|
+
|
612
|
+
def remove_tree(path)
|
613
|
+
if File.symlink?(path)
|
614
|
+
remove_file path
|
615
|
+
elsif File.dir?(path)
|
616
|
+
remove_tree0 path
|
617
|
+
else
|
618
|
+
force_remove_file path
|
619
|
+
end
|
620
|
+
end
|
621
|
+
|
622
|
+
def remove_tree0(path)
|
623
|
+
Dir.foreach(path) do |ent|
|
624
|
+
next if ent == '.'
|
625
|
+
next if ent == '..'
|
626
|
+
entpath = "#{path}/#{ent}"
|
627
|
+
if File.symlink?(entpath)
|
628
|
+
remove_file entpath
|
629
|
+
elsif File.dir?(entpath)
|
630
|
+
remove_tree0 entpath
|
631
|
+
else
|
632
|
+
force_remove_file entpath
|
633
|
+
end
|
634
|
+
end
|
635
|
+
begin
|
636
|
+
Dir.rmdir path
|
637
|
+
rescue Errno::ENOTEMPTY
|
638
|
+
# directory may not be empty
|
639
|
+
end
|
640
|
+
end
|
641
|
+
|
642
|
+
def move_file(src, dest)
|
643
|
+
force_remove_file dest
|
644
|
+
begin
|
645
|
+
File.rename src, dest
|
646
|
+
rescue
|
647
|
+
File.open(dest, 'wb') {|f|
|
648
|
+
f.write File.binread(src)
|
649
|
+
}
|
650
|
+
File.chmod File.stat(src).mode, dest
|
651
|
+
File.unlink src
|
652
|
+
end
|
653
|
+
end
|
654
|
+
|
655
|
+
def force_remove_file(path)
|
656
|
+
begin
|
657
|
+
remove_file path
|
658
|
+
rescue
|
659
|
+
end
|
660
|
+
end
|
661
|
+
|
662
|
+
def remove_file(path)
|
663
|
+
File.chmod 0777, path
|
664
|
+
File.unlink path
|
665
|
+
end
|
666
|
+
|
667
|
+
# === install
|
668
|
+
def install(from, dest, mode, prefix = nil)
|
669
|
+
$stderr.puts "install #{from} #{dest}" if verbose?
|
670
|
+
return if no_harm?
|
671
|
+
|
672
|
+
realdest = prefix ? prefix + File.expand_path(dest) : dest
|
673
|
+
realdest = File.join(realdest, File.basename(from)) if File.dir?(realdest)
|
674
|
+
str = File.binread(from)
|
675
|
+
if diff?(str, realdest)
|
676
|
+
verbose_off {
|
677
|
+
rm_f realdest if File.exist?(realdest)
|
678
|
+
}
|
679
|
+
begin
|
680
|
+
File.open(realdest, 'wb') {|f|
|
681
|
+
f.write(str)
|
682
|
+
}
|
683
|
+
rescue Errno::ENOENT => error
|
684
|
+
pp error
|
685
|
+
end
|
686
|
+
File.chmod(mode, realdest) if File.exist? realdest
|
687
|
+
|
688
|
+
File.open("#{objdir_root()}/InstalledFiles", 'a') {|f|
|
689
|
+
if prefix
|
690
|
+
f.puts realdest.sub(prefix, '')
|
691
|
+
else
|
692
|
+
f.puts realdest
|
693
|
+
end
|
694
|
+
}
|
695
|
+
end
|
696
|
+
end
|
697
|
+
|
698
|
+
# === diff?
|
699
|
+
def diff?(new_content, path)
|
700
|
+
return true unless File.exist?(path)
|
701
|
+
new_content != File.binread(path)
|
702
|
+
end
|
703
|
+
|
704
|
+
def command(*args)
|
705
|
+
$stderr.puts args.join(' ') if verbose?
|
706
|
+
system(*args) or raise RuntimeError,
|
707
|
+
"system(#{args.map{|a| a.inspect }.join(' ')}) failed"
|
708
|
+
end
|
709
|
+
|
710
|
+
def ruby(*args)
|
711
|
+
command config('rubyprog'), *args
|
712
|
+
end
|
713
|
+
|
714
|
+
def make(task = nil)
|
715
|
+
command(*[config('makeprog'), task].compact)
|
716
|
+
end
|
717
|
+
|
718
|
+
def extdir?(dir)
|
719
|
+
File.exist?("#{dir}/MANIFEST") or File.exist?("#{dir}/extconf.rb")
|
720
|
+
end
|
721
|
+
|
722
|
+
def files_of(dir)
|
723
|
+
Dir.open(dir) {|d|
|
724
|
+
return d.select {|ent| File.file?("#{dir}/#{ent}") }
|
725
|
+
}
|
726
|
+
end
|
727
|
+
|
728
|
+
DIR_REJECT = %w( . .. CVS SCCS RCS CVS.adm .svn )
|
729
|
+
|
730
|
+
def directories_of(dir)
|
731
|
+
Dir.open(dir) {|d|
|
732
|
+
return d.select {|ent| File.dir?("#{dir}/#{ent}") } - DIR_REJECT
|
733
|
+
}
|
734
|
+
end
|
735
|
+
|
736
|
+
end
|
737
|
+
|
738
|
+
|
739
|
+
# This module requires: #srcdir_root, #objdir_root, #relpath
|
740
|
+
module HookScriptAPI
|
741
|
+
|
742
|
+
def get_config(key)
|
743
|
+
@config[key]
|
744
|
+
end
|
745
|
+
|
746
|
+
alias config get_config
|
747
|
+
|
748
|
+
# obsolete: use metaconfig to change configuration
|
749
|
+
def set_config(key, val)
|
750
|
+
@config[key] = val
|
751
|
+
end
|
752
|
+
|
753
|
+
#
|
754
|
+
# srcdir/objdir (works only in the package directory)
|
755
|
+
#
|
756
|
+
|
757
|
+
def curr_srcdir
|
758
|
+
"#{srcdir_root()}/#{relpath()}"
|
759
|
+
end
|
760
|
+
|
761
|
+
def curr_objdir
|
762
|
+
"#{objdir_root()}/#{relpath()}"
|
763
|
+
end
|
764
|
+
|
765
|
+
def srcfile(path)
|
766
|
+
"#{curr_srcdir()}/#{path}"
|
767
|
+
end
|
768
|
+
|
769
|
+
def srcexist?(path)
|
770
|
+
File.exist?(srcfile(path))
|
771
|
+
end
|
772
|
+
|
773
|
+
def srcdirectory?(path)
|
774
|
+
File.dir?(srcfile(path))
|
775
|
+
end
|
776
|
+
|
777
|
+
def srcfile?(path)
|
778
|
+
File.file?(srcfile(path))
|
779
|
+
end
|
780
|
+
|
781
|
+
def srcentries(path = '.')
|
782
|
+
Dir.open("#{curr_srcdir()}/#{path}") {|d|
|
783
|
+
return d.to_a - %w(. ..)
|
784
|
+
}
|
785
|
+
end
|
786
|
+
|
787
|
+
def srcfiles(path = '.')
|
788
|
+
srcentries(path).select {|fname|
|
789
|
+
File.file?(File.join(curr_srcdir(), path, fname))
|
790
|
+
}
|
791
|
+
end
|
792
|
+
|
793
|
+
def srcdirectories(path = '.')
|
794
|
+
srcentries(path).select {|fname|
|
795
|
+
File.dir?(File.join(curr_srcdir(), path, fname))
|
796
|
+
}
|
797
|
+
end
|
798
|
+
|
799
|
+
end
|
800
|
+
|
801
|
+
|
802
|
+
class ToplevelInstaller
|
803
|
+
|
804
|
+
Version = '3.4.1'
|
805
|
+
Copyright = 'Copyright (c) 2000-2005 Minero Aoki'
|
806
|
+
|
807
|
+
TASKS = [
|
808
|
+
[ 'all', 'do config, setup, then install' ],
|
809
|
+
[ 'config', 'saves your configurations' ],
|
810
|
+
[ 'show', 'shows current configuration' ],
|
811
|
+
[ 'setup', 'compiles ruby extentions and others' ],
|
812
|
+
[ 'install', 'installs files' ],
|
813
|
+
[ 'test', 'run all tests in test/' ],
|
814
|
+
[ 'clean', "does `make clean' for each extention" ],
|
815
|
+
[ 'distclean',"does `make distclean' for each extention" ]
|
816
|
+
]
|
817
|
+
|
818
|
+
def ToplevelInstaller.invoke
|
819
|
+
config = ConfigTable.new(load_rbconfig())
|
820
|
+
config.load_standard_entries
|
821
|
+
config.load_multipackage_entries if multipackage?
|
822
|
+
config.fixup
|
823
|
+
klass = (multipackage?() ? ToplevelInstallerMulti : ToplevelInstaller)
|
824
|
+
klass.new(File.dirname($0), config).invoke
|
825
|
+
end
|
826
|
+
|
827
|
+
def ToplevelInstaller.multipackage?
|
828
|
+
File.dir?(File.dirname($0) + '/packages')
|
829
|
+
end
|
830
|
+
|
831
|
+
def ToplevelInstaller.load_rbconfig
|
832
|
+
if arg = ARGV.detect {|inner_arg| /\A--rbconfig=/ =~ inner_arg }
|
833
|
+
ARGV.delete(arg)
|
834
|
+
load File.expand_path(arg.split(/=/, 2)[1])
|
835
|
+
$".push 'rbconfig.rb'
|
836
|
+
else
|
837
|
+
require 'rbconfig'
|
838
|
+
end
|
839
|
+
::RbConfig::CONFIG
|
840
|
+
end
|
841
|
+
|
842
|
+
def initialize(ardir_root, config)
|
843
|
+
@ardir = File.expand_path(ardir_root)
|
844
|
+
@config = config
|
845
|
+
# cache
|
846
|
+
@valid_task_re = nil
|
847
|
+
end
|
848
|
+
|
849
|
+
# ========================================================================= #
|
850
|
+
# === config
|
851
|
+
# ========================================================================= #
|
852
|
+
def config(key)
|
853
|
+
@config[key]
|
854
|
+
end
|
855
|
+
|
856
|
+
def inspect
|
857
|
+
"#<#{self.class} #{__id__()}>"
|
858
|
+
end
|
859
|
+
|
860
|
+
def invoke
|
861
|
+
run_metaconfigs
|
862
|
+
case task = parsearg_global()
|
863
|
+
when nil, 'all'
|
864
|
+
parsearg_config
|
865
|
+
init_installers
|
866
|
+
exec_config
|
867
|
+
exec_setup
|
868
|
+
exec_install
|
869
|
+
else
|
870
|
+
case task
|
871
|
+
# === config
|
872
|
+
when 'config', 'test'
|
873
|
+
;
|
874
|
+
when 'clean', 'distclean'
|
875
|
+
@config.load_savefile if File.exist?(@config.savefile)
|
876
|
+
else
|
877
|
+
@config.load_savefile
|
878
|
+
end
|
879
|
+
__send__ "parsearg_#{task}"
|
880
|
+
init_installers
|
881
|
+
__send__ "exec_#{task}"
|
882
|
+
end
|
883
|
+
end
|
884
|
+
|
885
|
+
def run_metaconfigs
|
886
|
+
@config.load_script "#{@ardir}/metaconfig"
|
887
|
+
end
|
888
|
+
|
889
|
+
def init_installers
|
890
|
+
@installer = Installer.new(@config, @ardir, File.expand_path('.'))
|
891
|
+
end
|
892
|
+
|
893
|
+
#
|
894
|
+
# Hook Script API bases
|
895
|
+
#
|
896
|
+
|
897
|
+
def srcdir_root
|
898
|
+
@ardir
|
899
|
+
end
|
900
|
+
|
901
|
+
def objdir_root
|
902
|
+
'.'
|
903
|
+
end
|
904
|
+
|
905
|
+
def relpath
|
906
|
+
'.'
|
907
|
+
end
|
908
|
+
|
909
|
+
#
|
910
|
+
# Option Parsing
|
911
|
+
#
|
912
|
+
|
913
|
+
def parsearg_global
|
914
|
+
while arg = ARGV.shift
|
915
|
+
case arg
|
916
|
+
when /\A\w+\z/
|
917
|
+
setup_rb_error "invalid task: #{arg}" unless valid_task?(arg)
|
918
|
+
return arg
|
919
|
+
when '-q', '--quiet'
|
920
|
+
@config.verbose = false
|
921
|
+
when '--verbose'
|
922
|
+
@config.verbose = true
|
923
|
+
when '--help'
|
924
|
+
print_usage $stdout
|
925
|
+
exit 0
|
926
|
+
when '--version'
|
927
|
+
puts "#{File.basename($0)} version #{Version}"
|
928
|
+
exit 0
|
929
|
+
when '--copyright'
|
930
|
+
puts Copyright
|
931
|
+
exit 0
|
932
|
+
else
|
933
|
+
setup_rb_error "unknown global option '#{arg}'"
|
934
|
+
end
|
935
|
+
end
|
936
|
+
nil
|
937
|
+
end
|
938
|
+
|
939
|
+
def valid_task?(t)
|
940
|
+
valid_task_re() =~ t
|
941
|
+
end
|
942
|
+
|
943
|
+
def valid_task_re
|
944
|
+
@valid_task_re ||= /\A(?:#{TASKS.map {|task,desc| task }.join('|')})\z/
|
945
|
+
end
|
946
|
+
|
947
|
+
def parsearg_no_options
|
948
|
+
unless ARGV.empty?
|
949
|
+
task = caller(0).first.slice(%r<`parsearg_(\w+)'>, 1)
|
950
|
+
setup_rb_error "#{task}: unknown options: #{ARGV.join(' ')}"
|
951
|
+
end
|
952
|
+
end
|
953
|
+
|
954
|
+
alias parsearg_show parsearg_no_options
|
955
|
+
alias parsearg_setup parsearg_no_options
|
956
|
+
alias parsearg_test parsearg_no_options
|
957
|
+
alias parsearg_clean parsearg_no_options
|
958
|
+
alias parsearg_distclean parsearg_no_options
|
959
|
+
|
960
|
+
def parsearg_config
|
961
|
+
evalopt = []
|
962
|
+
set = []
|
963
|
+
@config.config_opt = []
|
964
|
+
while i = ARGV.shift
|
965
|
+
if /\A--?\z/ =~ i
|
966
|
+
@config.config_opt = ARGV.dup
|
967
|
+
break
|
968
|
+
end
|
969
|
+
name, value = *@config.parse_opt(i)
|
970
|
+
if @config.value_config?(name)
|
971
|
+
@config[name] = value
|
972
|
+
else
|
973
|
+
evalopt.push [name, value]
|
974
|
+
end
|
975
|
+
set.push name
|
976
|
+
end
|
977
|
+
evalopt.each do |inner_name, inner_value|
|
978
|
+
@config.lookup(inner_name).evaluate inner_value, @config
|
979
|
+
end
|
980
|
+
# Check if configuration is valid
|
981
|
+
set.each do |n|
|
982
|
+
@config[n] if @config.value_config?(n)
|
983
|
+
end
|
984
|
+
end
|
985
|
+
|
986
|
+
def parsearg_install
|
987
|
+
@config.no_harm = false
|
988
|
+
@config.install_prefix = ''
|
989
|
+
while a = ARGV.shift
|
990
|
+
case a
|
991
|
+
when '--no-harm'
|
992
|
+
@config.no_harm = true
|
993
|
+
when /\A--prefix=/
|
994
|
+
path = a.split(/=/, 2)[1]
|
995
|
+
path = File.expand_path(path) unless path[0,1] == '/'
|
996
|
+
@config.install_prefix = path
|
997
|
+
else
|
998
|
+
setup_rb_error "install: unknown option #{a}"
|
999
|
+
end
|
1000
|
+
end
|
1001
|
+
end
|
1002
|
+
|
1003
|
+
def print_usage(out)
|
1004
|
+
out.puts 'Typical Installation Procedure:'
|
1005
|
+
out.puts " $ ruby #{File.basename $0} config"
|
1006
|
+
out.puts " $ ruby #{File.basename $0} setup"
|
1007
|
+
out.puts " # ruby #{File.basename $0} install (may require root privilege)"
|
1008
|
+
out.puts
|
1009
|
+
out.puts 'Detailed Usage:'
|
1010
|
+
out.puts " ruby #{File.basename $0} <global option>"
|
1011
|
+
out.puts " ruby #{File.basename $0} [<global options>] <task> [<task options>]"
|
1012
|
+
|
1013
|
+
fmt = " %-24s %s\n"
|
1014
|
+
out.puts
|
1015
|
+
out.puts 'Global options:'
|
1016
|
+
out.printf fmt, '-q,--quiet', 'suppress message outputs'
|
1017
|
+
out.printf fmt, ' --verbose', 'output messages verbosely'
|
1018
|
+
out.printf fmt, ' --help', 'print this message'
|
1019
|
+
out.printf fmt, ' --version', 'print version and quit'
|
1020
|
+
out.printf fmt, ' --copyright', 'print copyright and quit'
|
1021
|
+
out.puts
|
1022
|
+
out.puts 'Tasks:'
|
1023
|
+
TASKS.each do |name, desc|
|
1024
|
+
out.printf fmt, name, desc
|
1025
|
+
end
|
1026
|
+
|
1027
|
+
fmt = " %-24s %s [%s]\n"
|
1028
|
+
out.puts
|
1029
|
+
out.puts 'Options for CONFIG or ALL:'
|
1030
|
+
@config.each do |item|
|
1031
|
+
out.printf fmt, item.help_opt, item.description, item.help_default
|
1032
|
+
end
|
1033
|
+
out.printf fmt, '--rbconfig=path', 'rbconfig.rb to load',"running ruby's"
|
1034
|
+
out.puts
|
1035
|
+
out.puts 'Options for INSTALL:'
|
1036
|
+
out.printf fmt, '--no-harm', 'only display what to do if given', 'off'
|
1037
|
+
out.printf fmt, '--prefix=path', 'install path prefix', ''
|
1038
|
+
out.puts
|
1039
|
+
end
|
1040
|
+
|
1041
|
+
#
|
1042
|
+
# Task Handlers
|
1043
|
+
#
|
1044
|
+
|
1045
|
+
def exec_config
|
1046
|
+
@installer.exec_config
|
1047
|
+
@config.save # must be final
|
1048
|
+
end
|
1049
|
+
|
1050
|
+
def exec_setup
|
1051
|
+
@installer.exec_setup
|
1052
|
+
end
|
1053
|
+
|
1054
|
+
def exec_install
|
1055
|
+
@installer.exec_install
|
1056
|
+
end
|
1057
|
+
|
1058
|
+
def exec_test
|
1059
|
+
@installer.exec_test
|
1060
|
+
end
|
1061
|
+
|
1062
|
+
def exec_show
|
1063
|
+
@config.each do |i|
|
1064
|
+
printf "%-20s %s\n", i.name, i.value if i.value?
|
1065
|
+
end
|
1066
|
+
end
|
1067
|
+
|
1068
|
+
def exec_clean
|
1069
|
+
@installer.exec_clean
|
1070
|
+
end
|
1071
|
+
|
1072
|
+
def exec_distclean
|
1073
|
+
@installer.exec_distclean
|
1074
|
+
end
|
1075
|
+
|
1076
|
+
end # class ToplevelInstaller
|
1077
|
+
|
1078
|
+
|
1079
|
+
class ToplevelInstallerMulti < ToplevelInstaller
|
1080
|
+
|
1081
|
+
include FileOperations
|
1082
|
+
|
1083
|
+
def initialize(ardir_root, config)
|
1084
|
+
super
|
1085
|
+
@packages = directories_of("#{@ardir}/packages")
|
1086
|
+
raise 'no package exists' if @packages.empty?
|
1087
|
+
@root_installer = Installer.new(@config, @ardir, File.expand_path('.'))
|
1088
|
+
end
|
1089
|
+
|
1090
|
+
def run_metaconfigs
|
1091
|
+
@config.load_script "#{@ardir}/metaconfig", self
|
1092
|
+
@packages.each do |name|
|
1093
|
+
@config.load_script "#{@ardir}/packages/#{name}/metaconfig"
|
1094
|
+
end
|
1095
|
+
end
|
1096
|
+
|
1097
|
+
attr_reader :packages
|
1098
|
+
|
1099
|
+
def packages=(list)
|
1100
|
+
raise 'package list is empty' if list.empty?
|
1101
|
+
list.each do |name|
|
1102
|
+
raise "directory packages/#{name} does not exist"\
|
1103
|
+
unless File.dir?("#{@ardir}/packages/#{name}")
|
1104
|
+
end
|
1105
|
+
@packages = list
|
1106
|
+
end
|
1107
|
+
|
1108
|
+
def init_installers
|
1109
|
+
@installers = {}
|
1110
|
+
@packages.each do |pack|
|
1111
|
+
@installers[pack] = Installer.new(@config,
|
1112
|
+
"#{@ardir}/packages/#{pack}",
|
1113
|
+
"packages/#{pack}")
|
1114
|
+
end
|
1115
|
+
with = extract_selection(config('with'))
|
1116
|
+
without = extract_selection(config('without'))
|
1117
|
+
@selected = @installers.keys.select {|name|
|
1118
|
+
(with.empty? or with.include?(name)) \
|
1119
|
+
and not without.include?(name)
|
1120
|
+
}
|
1121
|
+
end
|
1122
|
+
|
1123
|
+
def extract_selection(list)
|
1124
|
+
a = list.split(/,/)
|
1125
|
+
a.each do |name|
|
1126
|
+
setup_rb_error "no such package: #{name}" unless @installers.key?(name)
|
1127
|
+
end
|
1128
|
+
a
|
1129
|
+
end
|
1130
|
+
|
1131
|
+
def print_usage(f)
|
1132
|
+
super
|
1133
|
+
f.puts 'Inluded packages:'
|
1134
|
+
f.puts ' ' + @packages.sort.join(' ')
|
1135
|
+
f.puts
|
1136
|
+
end
|
1137
|
+
|
1138
|
+
#
|
1139
|
+
# Task Handlers
|
1140
|
+
#
|
1141
|
+
|
1142
|
+
def exec_config
|
1143
|
+
run_hook 'pre-config'
|
1144
|
+
each_selected_installers {|inst| inst.exec_config }
|
1145
|
+
run_hook 'post-config'
|
1146
|
+
@config.save # must be final
|
1147
|
+
end
|
1148
|
+
|
1149
|
+
def exec_setup
|
1150
|
+
run_hook 'pre-setup'
|
1151
|
+
each_selected_installers {|inst| inst.exec_setup }
|
1152
|
+
run_hook 'post-setup'
|
1153
|
+
end
|
1154
|
+
|
1155
|
+
def exec_install
|
1156
|
+
run_hook 'pre-install'
|
1157
|
+
each_selected_installers {|inst| inst.exec_install }
|
1158
|
+
run_hook 'post-install'
|
1159
|
+
end
|
1160
|
+
|
1161
|
+
def exec_test
|
1162
|
+
run_hook 'pre-test'
|
1163
|
+
each_selected_installers {|inst| inst.exec_test }
|
1164
|
+
run_hook 'post-test'
|
1165
|
+
end
|
1166
|
+
|
1167
|
+
def exec_clean
|
1168
|
+
rm_f @config.savefile
|
1169
|
+
run_hook 'pre-clean'
|
1170
|
+
each_selected_installers {|inst| inst.exec_clean }
|
1171
|
+
run_hook 'post-clean'
|
1172
|
+
end
|
1173
|
+
|
1174
|
+
def exec_distclean
|
1175
|
+
rm_f @config.savefile
|
1176
|
+
run_hook 'pre-distclean'
|
1177
|
+
each_selected_installers {|inst| inst.exec_distclean }
|
1178
|
+
run_hook 'post-distclean'
|
1179
|
+
end
|
1180
|
+
|
1181
|
+
#
|
1182
|
+
# lib
|
1183
|
+
#
|
1184
|
+
|
1185
|
+
def each_selected_installers
|
1186
|
+
Dir.mkdir 'packages' unless File.dir?('packages')
|
1187
|
+
@selected.each do |pack|
|
1188
|
+
$stderr.puts "Processing the package `#{pack}' ..." if verbose?
|
1189
|
+
Dir.mkdir "packages/#{pack}" unless File.dir?("packages/#{pack}")
|
1190
|
+
Dir.chdir "packages/#{pack}"
|
1191
|
+
yield @installers[pack]
|
1192
|
+
Dir.chdir '../..'
|
1193
|
+
end
|
1194
|
+
end
|
1195
|
+
|
1196
|
+
def run_hook(id)
|
1197
|
+
@root_installer.run_hook id
|
1198
|
+
end
|
1199
|
+
|
1200
|
+
# module FileOperations requires this
|
1201
|
+
def verbose?
|
1202
|
+
@config.verbose?
|
1203
|
+
end
|
1204
|
+
|
1205
|
+
# module FileOperations requires this
|
1206
|
+
def no_harm?
|
1207
|
+
@config.no_harm?
|
1208
|
+
end
|
1209
|
+
|
1210
|
+
end # class ToplevelInstallerMulti
|
1211
|
+
|
1212
|
+
|
1213
|
+
class Installer
|
1214
|
+
|
1215
|
+
FILETYPES = %w( bin lib ext data conf man )
|
1216
|
+
|
1217
|
+
include FileOperations
|
1218
|
+
include HookScriptAPI
|
1219
|
+
|
1220
|
+
def initialize(config, srcroot, objroot)
|
1221
|
+
@config = config
|
1222
|
+
@srcdir = File.expand_path(srcroot)
|
1223
|
+
@objdir = File.expand_path(objroot)
|
1224
|
+
@currdir = '.'
|
1225
|
+
end
|
1226
|
+
|
1227
|
+
def inspect
|
1228
|
+
"#<#{self.class} #{File.basename(@srcdir)}>"
|
1229
|
+
end
|
1230
|
+
|
1231
|
+
def noop(rel)
|
1232
|
+
end
|
1233
|
+
|
1234
|
+
#
|
1235
|
+
# Hook Script API base methods
|
1236
|
+
#
|
1237
|
+
|
1238
|
+
def srcdir_root
|
1239
|
+
@srcdir
|
1240
|
+
end
|
1241
|
+
|
1242
|
+
def objdir_root
|
1243
|
+
@objdir
|
1244
|
+
end
|
1245
|
+
|
1246
|
+
def relpath
|
1247
|
+
@currdir
|
1248
|
+
end
|
1249
|
+
|
1250
|
+
#
|
1251
|
+
# Config Access
|
1252
|
+
#
|
1253
|
+
|
1254
|
+
# module FileOperations requires this
|
1255
|
+
def verbose?
|
1256
|
+
@config.verbose?
|
1257
|
+
end
|
1258
|
+
|
1259
|
+
# module FileOperations requires this
|
1260
|
+
def no_harm?
|
1261
|
+
@config.no_harm?
|
1262
|
+
end
|
1263
|
+
|
1264
|
+
def verbose_off
|
1265
|
+
begin
|
1266
|
+
save, @config.verbose = @config.verbose?, false
|
1267
|
+
yield
|
1268
|
+
ensure
|
1269
|
+
@config.verbose = save
|
1270
|
+
end
|
1271
|
+
end
|
1272
|
+
|
1273
|
+
#
|
1274
|
+
# TASK config
|
1275
|
+
#
|
1276
|
+
|
1277
|
+
def exec_config
|
1278
|
+
exec_task_traverse 'config'
|
1279
|
+
end
|
1280
|
+
|
1281
|
+
alias config_dir_bin noop
|
1282
|
+
alias config_dir_lib noop
|
1283
|
+
|
1284
|
+
def config_dir_ext(rel)
|
1285
|
+
extconf if extdir?(curr_srcdir())
|
1286
|
+
end
|
1287
|
+
|
1288
|
+
alias config_dir_data noop
|
1289
|
+
alias config_dir_conf noop
|
1290
|
+
alias config_dir_man noop
|
1291
|
+
|
1292
|
+
def extconf
|
1293
|
+
ruby "#{curr_srcdir()}/extconf.rb", *@config.config_opt
|
1294
|
+
end
|
1295
|
+
|
1296
|
+
#
|
1297
|
+
# TASK setup
|
1298
|
+
#
|
1299
|
+
|
1300
|
+
def exec_setup
|
1301
|
+
exec_task_traverse 'setup'
|
1302
|
+
end
|
1303
|
+
|
1304
|
+
def setup_dir_bin(rel)
|
1305
|
+
# files_of(curr_srcdir()).each do |fname|
|
1306
|
+
# update_shebang_line "#{curr_srcdir()}/#{fname}"
|
1307
|
+
# end # The above line was modifed by shevy Sep 2014.
|
1308
|
+
end
|
1309
|
+
|
1310
|
+
alias setup_dir_lib noop
|
1311
|
+
|
1312
|
+
def setup_dir_ext(rel)
|
1313
|
+
make if extdir?(curr_srcdir())
|
1314
|
+
end
|
1315
|
+
|
1316
|
+
alias setup_dir_data noop
|
1317
|
+
alias setup_dir_conf noop
|
1318
|
+
alias setup_dir_man noop
|
1319
|
+
|
1320
|
+
def update_shebang_line(path)
|
1321
|
+
return if no_harm?
|
1322
|
+
return if config('shebang') == 'never'
|
1323
|
+
old = Shebang.load(path)
|
1324
|
+
if old
|
1325
|
+
$stderr.puts "warning: #{path}: Shebang line includes too many args. It is not portable and your program may not work." if old.args.size > 1
|
1326
|
+
new = new_shebang(old)
|
1327
|
+
return if new.to_s == old.to_s
|
1328
|
+
else
|
1329
|
+
return unless config('shebang') == 'all'
|
1330
|
+
new = Shebang.new(config('rubypath'))
|
1331
|
+
end
|
1332
|
+
$stderr.puts "updating shebang: #{File.basename(path)}" if verbose?
|
1333
|
+
open_atomic_writer(path) {|output|
|
1334
|
+
File.open(path, 'rb') {|f|
|
1335
|
+
f.gets if old # discard
|
1336
|
+
output.puts new.to_s
|
1337
|
+
output.print f.read
|
1338
|
+
}
|
1339
|
+
}
|
1340
|
+
end
|
1341
|
+
|
1342
|
+
def new_shebang(old)
|
1343
|
+
if /\Aruby/ =~ File.basename(old.cmd)
|
1344
|
+
Shebang.new(config('rubypath'), old.args)
|
1345
|
+
elsif File.basename(old.cmd) == 'env' and old.args.first == 'ruby'
|
1346
|
+
Shebang.new(config('rubypath'), old.args[1..-1])
|
1347
|
+
else
|
1348
|
+
return old unless config('shebang') == 'all'
|
1349
|
+
Shebang.new(config('rubypath'))
|
1350
|
+
end
|
1351
|
+
end
|
1352
|
+
|
1353
|
+
def open_atomic_writer(path, &block)
|
1354
|
+
tmpfile = File.basename(path) + '.tmp'
|
1355
|
+
begin
|
1356
|
+
File.open(tmpfile, 'wb', &block)
|
1357
|
+
File.rename tmpfile, File.basename(path)
|
1358
|
+
ensure
|
1359
|
+
File.unlink tmpfile if File.exist?(tmpfile)
|
1360
|
+
end
|
1361
|
+
end
|
1362
|
+
|
1363
|
+
class Shebang
|
1364
|
+
def Shebang.load(path)
|
1365
|
+
line = nil
|
1366
|
+
File.open(path) {|f|
|
1367
|
+
line = f.gets
|
1368
|
+
}
|
1369
|
+
return nil unless /\A#!/ =~ line
|
1370
|
+
parse(line)
|
1371
|
+
end
|
1372
|
+
|
1373
|
+
def Shebang.parse(line)
|
1374
|
+
cmd, *args = *line.strip.sub(/\A\#!/, '').split(' ')
|
1375
|
+
new(cmd, args)
|
1376
|
+
end
|
1377
|
+
|
1378
|
+
def initialize(cmd, args = [])
|
1379
|
+
@cmd = cmd
|
1380
|
+
@args = args
|
1381
|
+
end
|
1382
|
+
|
1383
|
+
attr_reader :cmd
|
1384
|
+
attr_reader :args
|
1385
|
+
|
1386
|
+
def to_s
|
1387
|
+
"#! #{@cmd}" + (@args.empty? ? '' : " #{@args.join(' ')}")
|
1388
|
+
end
|
1389
|
+
end
|
1390
|
+
|
1391
|
+
#
|
1392
|
+
# TASK install
|
1393
|
+
#
|
1394
|
+
|
1395
|
+
GLOB2REGEX = {
|
1396
|
+
'.' => '\.',
|
1397
|
+
'$' => '\$',
|
1398
|
+
'#' => '\#',
|
1399
|
+
'*' => '.*'
|
1400
|
+
}
|
1401
|
+
|
1402
|
+
def exec_install
|
1403
|
+
rm_f 'InstalledFiles'
|
1404
|
+
exec_task_traverse 'install'
|
1405
|
+
end
|
1406
|
+
|
1407
|
+
# ========================================================================= #
|
1408
|
+
# === install_dir_bin
|
1409
|
+
# ========================================================================= #
|
1410
|
+
def install_dir_bin(rel)
|
1411
|
+
install_files targetfiles(), "#{config('bindir')}/#{rel}", 0755
|
1412
|
+
end
|
1413
|
+
|
1414
|
+
def install_dir_lib(rel)
|
1415
|
+
install_files libfiles(), "#{config('rbdir')}/#{rel}", 0644
|
1416
|
+
end
|
1417
|
+
|
1418
|
+
def install_dir_ext(rel)
|
1419
|
+
return unless extdir?(curr_srcdir())
|
1420
|
+
install_files rubyextentions('.'),
|
1421
|
+
"#{config('sodir')}/#{File.dirname(rel)}",
|
1422
|
+
0555
|
1423
|
+
end
|
1424
|
+
|
1425
|
+
def install_dir_data(rel)
|
1426
|
+
install_files targetfiles(), "#{config('datadir')}/#{rel}", 0644
|
1427
|
+
end
|
1428
|
+
|
1429
|
+
def install_dir_conf(rel)
|
1430
|
+
# FIXME: should not remove current config files
|
1431
|
+
# (rename previous file to .old/.org)
|
1432
|
+
install_files targetfiles(), "#{config('sysconfdir')}/#{rel}", 0644
|
1433
|
+
end
|
1434
|
+
|
1435
|
+
def install_dir_man(rel)
|
1436
|
+
install_files targetfiles(), "#{config('mandir')}/#{rel}", 0644
|
1437
|
+
end
|
1438
|
+
|
1439
|
+
def install_files(list, dest, mode)
|
1440
|
+
mkdir_p dest, @config.install_prefix
|
1441
|
+
list.each { |fname|
|
1442
|
+
install fname, dest, mode, @config.install_prefix
|
1443
|
+
}
|
1444
|
+
end
|
1445
|
+
|
1446
|
+
def libfiles
|
1447
|
+
glob_reject(%w(*.y *.output), targetfiles())
|
1448
|
+
end
|
1449
|
+
|
1450
|
+
def rubyextentions(dir)
|
1451
|
+
ents = glob_select("*.#{@config.dllext}", targetfiles())
|
1452
|
+
if ents.empty?
|
1453
|
+
setup_rb_error "no ruby extention exists: 'ruby #{$0} setup' first"
|
1454
|
+
end
|
1455
|
+
ents
|
1456
|
+
end
|
1457
|
+
|
1458
|
+
def targetfiles
|
1459
|
+
mapdir(existfiles() - hookfiles())
|
1460
|
+
end
|
1461
|
+
|
1462
|
+
def mapdir(ents)
|
1463
|
+
ents.map {|ent|
|
1464
|
+
if File.exist?(ent)
|
1465
|
+
then ent # objdir
|
1466
|
+
else "#{curr_srcdir()}/#{ent}" # srcdir
|
1467
|
+
end
|
1468
|
+
}
|
1469
|
+
end
|
1470
|
+
|
1471
|
+
# picked up many entries from cvs-1.11.1/src/ignore.c
|
1472
|
+
JUNK_FILES = %w(
|
1473
|
+
core RCSLOG tags TAGS .make.state
|
1474
|
+
.nse_depinfo #* .#* cvslog.* ,* .del-* *.olb
|
1475
|
+
*~ *.old *.bak *.BAK *.orig *.rej _$* *$
|
1476
|
+
|
1477
|
+
*.org *.in .*
|
1478
|
+
)
|
1479
|
+
|
1480
|
+
def existfiles
|
1481
|
+
glob_reject(JUNK_FILES, (files_of(curr_srcdir()) | files_of('.')))
|
1482
|
+
end
|
1483
|
+
|
1484
|
+
def hookfiles
|
1485
|
+
%w( pre-%s post-%s pre-%s.rb post-%s.rb ).map {|fmt|
|
1486
|
+
%w( config setup install clean ).map {|t| sprintf(fmt, t) }
|
1487
|
+
}.flatten
|
1488
|
+
end
|
1489
|
+
|
1490
|
+
def glob_select(pat, ents)
|
1491
|
+
re = globs2re([pat])
|
1492
|
+
ents.select {|ent| re =~ ent }
|
1493
|
+
end
|
1494
|
+
|
1495
|
+
# ========================================================================= #
|
1496
|
+
# === glob_reject
|
1497
|
+
# ========================================================================= #
|
1498
|
+
def glob_reject(pats, ents)
|
1499
|
+
re = globs2re(pats)
|
1500
|
+
begin
|
1501
|
+
ents.reject {|ent| re =~ ent }
|
1502
|
+
rescue ArgumentError => error
|
1503
|
+
pp error
|
1504
|
+
end
|
1505
|
+
end
|
1506
|
+
|
1507
|
+
def globs2re(pats)
|
1508
|
+
/\A(?:#{
|
1509
|
+
pats.map {|pat| pat.gsub(/[\.\$\#\*]/) {|ch| GLOB2REGEX[ch] } }.join('|')
|
1510
|
+
})\z/
|
1511
|
+
end
|
1512
|
+
|
1513
|
+
#
|
1514
|
+
# TASK test
|
1515
|
+
#
|
1516
|
+
|
1517
|
+
TESTDIR = 'test'
|
1518
|
+
|
1519
|
+
def exec_test
|
1520
|
+
unless File.directory?('test')
|
1521
|
+
$stderr.puts 'no test in this package' if verbose?
|
1522
|
+
return
|
1523
|
+
end
|
1524
|
+
$stderr.puts 'Running tests...' if verbose?
|
1525
|
+
begin
|
1526
|
+
require 'test/unit'
|
1527
|
+
rescue LoadError
|
1528
|
+
setup_rb_error 'test/unit cannot loaded. You need Ruby 1.8 or later to invoke this task.'
|
1529
|
+
end
|
1530
|
+
runner = Test::Unit::AutoRunner.new(true)
|
1531
|
+
runner.to_run << TESTDIR
|
1532
|
+
runner.run
|
1533
|
+
end
|
1534
|
+
|
1535
|
+
#
|
1536
|
+
# TASK clean
|
1537
|
+
#
|
1538
|
+
|
1539
|
+
def exec_clean
|
1540
|
+
exec_task_traverse 'clean'
|
1541
|
+
rm_f @config.savefile
|
1542
|
+
rm_f 'InstalledFiles'
|
1543
|
+
end
|
1544
|
+
|
1545
|
+
alias clean_dir_bin noop
|
1546
|
+
alias clean_dir_lib noop
|
1547
|
+
alias clean_dir_data noop
|
1548
|
+
alias clean_dir_conf noop
|
1549
|
+
alias clean_dir_man noop
|
1550
|
+
|
1551
|
+
def clean_dir_ext(rel)
|
1552
|
+
return unless extdir?(curr_srcdir())
|
1553
|
+
make 'clean' if File.file?('Makefile')
|
1554
|
+
end
|
1555
|
+
|
1556
|
+
#
|
1557
|
+
# TASK distclean
|
1558
|
+
#
|
1559
|
+
|
1560
|
+
def exec_distclean
|
1561
|
+
exec_task_traverse 'distclean'
|
1562
|
+
rm_f @config.savefile
|
1563
|
+
rm_f 'InstalledFiles'
|
1564
|
+
end
|
1565
|
+
|
1566
|
+
alias distclean_dir_bin noop
|
1567
|
+
alias distclean_dir_lib noop
|
1568
|
+
|
1569
|
+
def distclean_dir_ext(rel)
|
1570
|
+
return unless extdir?(curr_srcdir())
|
1571
|
+
make 'distclean' if File.file?('Makefile')
|
1572
|
+
end
|
1573
|
+
|
1574
|
+
alias distclean_dir_data noop
|
1575
|
+
alias distclean_dir_conf noop
|
1576
|
+
alias distclean_dir_man noop
|
1577
|
+
|
1578
|
+
#
|
1579
|
+
# Traversing
|
1580
|
+
#
|
1581
|
+
|
1582
|
+
def exec_task_traverse(task)
|
1583
|
+
run_hook "pre-#{task}"
|
1584
|
+
FILETYPES.each do |type|
|
1585
|
+
if type == 'ext' and config('without-ext') == 'yes'
|
1586
|
+
$stderr.puts 'skipping ext/* by user option' if verbose?
|
1587
|
+
next
|
1588
|
+
end
|
1589
|
+
traverse task, type, "#{task}_dir_#{type}"
|
1590
|
+
end
|
1591
|
+
run_hook "post-#{task}"
|
1592
|
+
end
|
1593
|
+
|
1594
|
+
# ========================================================================= #
|
1595
|
+
# === traverse
|
1596
|
+
#
|
1597
|
+
# This method can fail when it comes to Encoding-related issues.
|
1598
|
+
# ========================================================================= #
|
1599
|
+
def traverse(task, rel, mid)
|
1600
|
+
dive_into(rel) {
|
1601
|
+
run_hook "pre-#{task}"
|
1602
|
+
__send__(mid, rel.sub(%r[\A.*?(?:/|\z)], ''))
|
1603
|
+
directories_of(curr_srcdir()).each { |d|
|
1604
|
+
traverse task, "#{rel}/#{d}", mid
|
1605
|
+
}
|
1606
|
+
run_hook "post-#{task}"
|
1607
|
+
}
|
1608
|
+
end
|
1609
|
+
|
1610
|
+
def dive_into(rel)
|
1611
|
+
return unless File.dir?("#{@srcdir}/#{rel}")
|
1612
|
+
|
1613
|
+
dir = File.basename(rel)
|
1614
|
+
Dir.mkdir dir unless File.dir?(dir)
|
1615
|
+
prevdir = Dir.pwd
|
1616
|
+
Dir.chdir dir
|
1617
|
+
$stderr.puts '---> ' + rel if verbose?
|
1618
|
+
@currdir = rel
|
1619
|
+
yield
|
1620
|
+
Dir.chdir prevdir
|
1621
|
+
$stderr.puts '<--- ' + rel if verbose?
|
1622
|
+
@currdir = File.dirname(rel)
|
1623
|
+
end
|
1624
|
+
|
1625
|
+
def run_hook(id)
|
1626
|
+
path = [ "#{curr_srcdir()}/#{id}",
|
1627
|
+
"#{curr_srcdir()}/#{id}.rb" ].detect {|cand| File.file?(cand) }
|
1628
|
+
return unless path
|
1629
|
+
begin
|
1630
|
+
instance_eval File.read(path), path, 1
|
1631
|
+
rescue
|
1632
|
+
raise if $DEBUG
|
1633
|
+
setup_rb_error "hook #{path} failed:\n" + $!.message
|
1634
|
+
end
|
1635
|
+
end
|
1636
|
+
|
1637
|
+
end # class Installer
|
1638
|
+
|
1639
|
+
|
1640
|
+
class SetupError < StandardError; end
|
1641
|
+
|
1642
|
+
def setup_rb_error(msg)
|
1643
|
+
raise SetupError, msg
|
1644
|
+
end
|
1645
|
+
|
1646
|
+
if $0 == __FILE__
|
1647
|
+
begin
|
1648
|
+
ToplevelInstaller.invoke
|
1649
|
+
rescue SetupError
|
1650
|
+
raise if $DEBUG
|
1651
|
+
$stderr.puts $!.message
|
1652
|
+
$stderr.puts "Try 'ruby #{$0} --help' for detailed usage."
|
1653
|
+
exit 1
|
1654
|
+
end
|
1655
|
+
end
|