bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/shell/shell.rb

@@ -3,39 +3,1148 @@
 # frozen_string_literal: true
 # =========================================================================== #
 # === Bioroebe::Shell
+#
+# This shell wraps together all related Bio tasks. It contains
+# the core-functionality for the Bioroebe::Shell interface.
+#
+# To use it in one of your projects, do:
+#
+#   require 'bioroebe'; Bioroebe::Shell.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/shell/menu.rb'
+# require 'bioroebe/shell/shell.rb'
 # =========================================================================== #
 require 'bioroebe/base/commandline_application/commandline_application.rb'
+
+module Bioroebe
+
+class Shell < ::Bioroebe::CommandlineApplication # === Bioroebe::Shell
+
+  alias ee print
+
+  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+  require 'bioroebe/codons/convert_this_codon_to_that_aminoacid.rb'
+
+  # ========================================================================= #
+  # Various failsave requires will be pulled in next. This includes the
+  # chemistry_paradise gem, if it is available.
+  # ========================================================================= #
+  array_failsave_requires = %w(
+    chemistry_paradise
+    directory_paradise
+    easycompile
+    rcfiles
+    xorg_buffer/module
+  )
+  array_failsave_requires.each {|project|
+    begin
+      require project
+    rescue LoadError; end # Silent rescue.
+  }
+
+  if Bioroebe.is_on_roebe?
+    # ======================================================================= #
+    # Load up support for FtpParadise, but only on roebe-systems.
+    # ======================================================================= #
+    begin
+      require 'ftp_paradise'
+    rescue LoadError; end
+  end
+
+  require 'bioroebe/configuration/configuration.rb'
+  require 'bioroebe/project/project.rb'
+  require 'bioroebe/conversions/dna_to_aminoacid_sequence.rb'
+  require 'bioroebe/constants/files_and_directories.rb'
+  require 'bioroebe/constants/misc.rb'
+  require 'bioroebe/codons/show_codon_usage.rb'
+  require 'bioroebe/codons/show_this_codon_table.rb'
+  require 'bioroebe/calculate/calculate_levensthein_distance.rb'
+  require 'bioroebe/nucleotides/molecular_weight_of_nucleotides.rb'
+  require 'bioroebe/nucleotides/show_nucleotide_sequence.rb'
+  require 'bioroebe/count/count_amount_of_aminoacids.rb'
+  require 'bioroebe/parsers/blosum_parser.rb'
+  require 'bioroebe/sequence/sequence.rb'
+  require 'bioroebe/string_matching/find_longest_substring.rb'
+  require 'bioroebe/enzymes/has_this_restriction_enzyme.rb'
+  require 'bioroebe/enzymes/restriction_enzymes_file.rb'
+  require 'bioroebe/shell/colours/colours.rb'
+  require 'bioroebe/shell/readline/readline.rb' # ← Needed in this file here.
+  require 'bioroebe/shell/menu.rb'
+  require 'bioroebe/shell/misc.rb'
+  # ========================================================================= #
+  # Next, require bioroebe/utility_scripts/ - this is important for the
+  # menu() interface:
+  # ========================================================================= #
+  require 'bioroebe/utility_scripts/display_open_reading_frames/display_open_reading_frames.rb'
+  # ========================================================================= #
+  # Next, batch-require all toplevel_methods/ from the bioroebe project:
+  # ========================================================================= #
+  require 'bioroebe/requires/require_the_toplevel_methods.rb'
+  # require 'bioroebe/toplevel_methods/map_ncbi_entry_to_eutils_id.rb'
+  # require 'bioroebe/toplevel_methods/matches.rb'
+  # require 'bioroebe/toplevel_methods/taxonomy.rb'
+  # require 'bioroebe/toplevel_methods/download_and_fetch_data.rb'
+
+  # ========================================================================= #
+  # === HOME_DIRECTORY_OF_USER_X
+  #
+  # Hardcoded path - only useful on my home setup, though.
+  # ========================================================================= #
+  HOME_DIRECTORY_OF_USER_X = '/home/x/'
+
+  # ========================================================================= #
+  # === RUBY_SRC
+  #
+  # Hardcoded. This is only useful on my home system.
+  # ========================================================================= #
+  if ENV['RSRC']
+    RUBY_SRC = "#{ENV['RSRC']}/"
+  else
+    RUBY_SRC = "#{HOME_DIRECTORY_OF_USER_X}programming/ruby/src/"
+  end
+
+  # ========================================================================= #
+  # === RUBY_BIOROEBE
+  #
+  # This allows a user to designate another home directory.
+  # ========================================================================= #
+  if ENV['RUBY_BIOROEBE']
+    BIOROEBE = ENV['RUBY_BIOROEBE'].to_s
+  else
+    BIOROEBE = ENV['HOME']
+  end
+
+  # ========================================================================= #
+  # === FILE_USE_SILENT_STARTUP
+  # ========================================================================= #
+  FILE_USE_SILENT_STARTUP = 
+    "#{::Bioroebe.project_base_directory?}shell/configuration/use_silent_startup.yml"
+
+  # ========================================================================= #
+  # === SHALL_WE_DEBUG
+  # ========================================================================= #
+  SHALL_WE_DEBUG = false
+
+  # ========================================================================= #
+  # === TRUNCATE_AT_N_ELEMENTS
+  #
+  # If we display nucleotide strings, then by default, these may be very
+  # long. So the following constant will act as a threshold.
+  # ========================================================================= #
+  TRUNCATE_AT_N_ELEMENTS = 2000
+
+  # ========================================================================= #
+  # === BIOSHELL_SAVE_FILE
+  #
+  # Designate the default location for the save-file, a markdown file.
+  # ========================================================================= #
+  if Dir.exist? ::Bioroebe.log_dir?
+    BIOSHELL_SAVE_FILE = "#{::Bioroebe.log_dir?}shell_file.md"
+  else
+    BIOSHELL_SAVE_FILE = '/home/Temp/bioroebe/shell_file.md'
+  end
+
+  # ========================================================================= #
+  # === HOME_DIR
+  #
+  # This probably is not used a lot anymore these days.
+  # ========================================================================= #
+  if RUBY_SRC # This is valid at home.
+    HOME_DIR = "#{ENV['RSRC']}/bioroebe/lib/bioroebe/"
+  else
+    begin
+      home_dir = File.expand_path('~')
+    rescue Exception
+      home_dir = '/root/'
+    end
+    HOME_DIR = home_dir+'.gem/gems/bioroebe-'+
+               Bioroebe.version?.to_s+'/lib/bioroebe/'
+  end
+
+  # ========================================================================= #
+  # === DEFAULT_PADDING
+  # ========================================================================= #
+  DEFAULT_PADDING = '  ' # This is left-padding.
+
+  # ========================================================================= #
+  # === MAIN_EDITOR
+  #
+  # Which editor to use.
+  # ========================================================================= #
+  if ENV['IS_ROEBE']
+    MAIN_EDITOR = 'bluefish'
+  else # else assume that we may be on windows. 
+    MAIN_EDITOR = 'notepad++.exe'
+  end; MY_EDITOR = MAIN_EDITOR # === MY_EDITOR
+
+  _ = ::Bioroebe.project_yaml_directory?+
+      'default_dna_input.yml' # cat $RUBY_BIO/YAML/default_dna_input.yml
+  # ========================================================================= #
+  # === DEFAULT_DNA_INPUT_YAML_FILE
+  # ========================================================================= #
+  DEFAULT_DNA_INPUT_YAML_FILE = YAML.load_file(_) if File.exist? _
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV
+    )
+    reset
+    set_commandline_arguments(commandline_arguments)
+    # ======================================================================= #
+    # Intercept some important commandline arguments next.
+    # ======================================================================= #
+    case first?
+    # ======================================================================= #
+    # === bioshell --controller
+    # ======================================================================= #
+    when /^-?-?controller$/i
+      require 'bioroebe/gui/gtk3/controller/controller.rb'
+      ::Bioroebe.run_gtk_controller
+      exit_program
+    # ======================================================================= #
+    # === bioshell --do-not-create-directories-on-startup
+    # === bioshell --do-not-create-directories
+    #
+    # Do not create directories on startup.
+    #
+    # Invocation example:
+    #
+    #   bioshell --do-not-create-directories-on-startup
+    #
+    # ======================================================================= #
+    when /^-?-?do(-|_| )?not(-|_| )?create(-|_| )?directories(-|_| )?on(-|_| )?startup$/i,
+         /^-?-?do(-|_| )?not(-|_| )?create(-|_| )?directories$/i
+      @internal_hash[:create_directories_on_startup_of_the_shell] = false
+    # ======================================================================= #
+    # === bioroebe --protein-to-dna
+    #
+    # This entry point will try to start the ruby-gtk3 protein-to-DNA
+    # converting widget.
+    # ======================================================================= #
+    when /^-?-?protein(-|_| )?to(-|_| )?dna$/i
+      require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
+      ::Bioroebe::GUI::Gtk::ProteinToDNA.run_gtk3_widget
+      exit
+    # ======================================================================= #
+    # === bioroebe --help
+    #
+    # This entry-point will quickly show which options are available for
+    # the bioshell.
+    # ======================================================================= #
+    when /^-?-?help$/
+      show_commandline_options
+    # ======================================================================= #
+    # === bioshell --permanently-disable-startup-intro
+    # === bioshell --permanently-disable-startup-notice
+    # === bioshell --permanently-no-startup-intro
+    # === bioshell --permanently-no-startup-info
+    # ======================================================================= #
+    when /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?intro$/,
+         /^-?-?permanently(-|_)?disable(-|_)?startup(-|_)?notice$/,
+         /^-?-?permanently(-|_)?no(-|_)?startup(-|_)?intro$/,
+         /^-?-?permanently(-|_)?no(-|_)?startup(-|_)?info$/
+      permanently_disable_startup_intro
+    # ======================================================================= #
+    # === :no_commandline_arguments
+    # ======================================================================= #
+    when :no_commandline_arguments
+      # ===================================================================== #
+      # Simply pass through in this case.
+      # ===================================================================== #
+    # ======================================================================= #
+    # === :exit_gracefully
+    # ======================================================================= #
+    when :exit_gracefully
+      set_exit_gracefully
+    # ======================================================================= #
+    # === bioroebe --silent-startup
+    # ======================================================================= #
+    when /^-?-?silent(-|_)?startup$/,
+         /^-?-?silent$/
+      do_a_silent_startup
+    # ======================================================================= #
+    # === bioroebe --random-aminoacids=33
+    # === bioroebe --n-aminoacids=33
+    # ======================================================================= #
+    when /^-?-?random(-|_)?aminoacids=(.+)$/i,
+         /^-?-?n(-|_)?aminoacids=(.+)$/i
+      n_aminoacids = $2.to_s.dup
+      ::Bioroebe.create_random_aminoacids(n_aminoacids) { :do_report }
+      exit
+    # ======================================================================= #
+    # === bioroebe --rnafold=cdna.MT.fa
+    # ======================================================================= #
+    when /^-?-?rnafold=(.+)$/
+      try_to_run_rnalfold_on_this_file($1.to_s.dup)
+      exit
+    # ======================================================================= #
+    # === bioroebe --fasta=/Depot/Bioroebe/Arabidopsis_thaliana_chromosome_5_sequence.fasta
+    # ======================================================================= #
+    when /^-?-?fasta=(.+)$/
+      this_fasta_file = $1.to_s.dup
+      if File.exist?
+        handle_fasta(this_fasta_file)
+      else
+        e 'No file could be found at `'+sfile(this_fasta_file)+'`.'
+      end
+    # ======================================================================= #
+    # === bioroebe --n-fasta-entries
+    #
+    # Usage example:
+    #
+    #   cd /root/Bioroebe/Downloads/; bioroebe --n-fasta-entries
+    #
+    # ======================================================================= #
+    when /^-?-?n(-|_)?fasta(-|_)?entries$/
+      require 'bioroebe/fasta/display_how_many_fasta_entries_are_in_this_directory.rb'
+      ::Bioroebe::DisplayHowManyFastaEntriesAreInThisDirectory.new
+      exit
+    # ======================================================================= #
+    # === bioroebe --split-this-fasta-file-into-chromosomes=Mus_musculus.GRCm38.ncrna.fa
+    # ======================================================================= #
+    when /^-?-?split(-|_)?this(-|_)?fasta(-|_)?file(-|_)?into(-|_)?chromosomes=(.+)$/i # $6
+      _ = $6.to_s.dup
+      require 'bioroebe/fasta/split_this_fasta_file_into_chromosomes/split_this_fasta_file_into_chromosomes.rb'
+      ::Bioroebe::SplitThisFastaFileIntoChromosomes.new(_)
+      exit
+    # ======================================================================= #
+    # === bioroebe --stats
+    #
+    # This entry-point will show some simple fasta-statistics, from
+    # the current directory.
+    #
+    # Usage example:
+    #
+    #   cd /root/Bioroebe/Downloads/; bioroebe --stats
+    #
+    # ======================================================================= #
+    when /^-?-?stats$/i,
+         /^-?-?statistics$/i,
+         /^-?-?fasta(-|_)?stats$/i
+      require 'bioroebe/fasta/show_fasta_statistics.rb'
+      ::Bioroebe.show_fasta_statistics(Dir['*'])
+      exit
+    # ======================================================================= #
+    # === bioroebe --download=ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
+    #
+    # This entry point allows us to download a remote program.
+    #
+    # Invocation example:
+    #
+    #   bioroebe --download=ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
+    #   bioroebe --download ftp://ftp.ensembl.org/pub/release-92/gtf/mus_musculus/
+    #
+    # Note that the second variant currently (April 2020) does not work -
+    # let's see if we need it again in the future.
+    # ======================================================================= #
+    when /^-?-?download=(.+)/
+      ::Bioroebe.download($1.to_s.dup)
+    # ======================================================================= #
+    # === bioroebe --sequence=150
+    #
+    # This entry point allows us to use any sequence, on startup.
+    #
+    # Invocation example:
+    #
+    #   bioroebe --sequence=1505
+    #
+    # ======================================================================= #
+    when /^-?-?sequence (.+)/,
+         /^-?-?sequence=(.+)/
+      set_dna($1.to_s.dup, :be_quiet) # Be quiet here when doing the assignment.
+    # ======================================================================= #
+    # === bioroebe --show-exon-statistics-for=/tmp/praktikum/Mouse/chromosome_8/parsed/cdna.8.L100.global.gtf
+    # ======================================================================= #
+    when /^-?-?show(-|_)?exon(-|_)?statistics(-|_)?for=(.+)$/ # === $4
+      ::Bioroebe.show_exon_statistics($4.to_s.dup)
+      exit
+    # ======================================================================= #
+    # === bioroebe --sinatra
+    # ======================================================================= #
+    when /^-?-?sinatra$/i
+      do_start_the_sinatra_interface
+      return
+    end
+    run
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset(
+      be_verbose = true
+    )
+    super()
+    infer_the_namespace
+    reset_to_initial_state(be_verbose)
+    # ======================================================================= #
+    # Next, we have to try to enable the configuration.
+    # ======================================================================= #
+    enable_configuration
+    # ======================================================================= #
+    # Make sure that the base directories exist, within reset().
+    # ======================================================================= #
+    ensure_that_the_base_directories_exist
+    set_default_length # Set the default length of 1000 here.
+    if defined? DEFAULT_DNA_INPUT_YAML_FILE # Main DNA string.
+      set_string(DEFAULT_DNA_INPUT_YAML_FILE)
+    end
+  end
+
+  # ========================================================================= #
+  # === reset_to_initial_state
+  # ========================================================================= #
+  def reset_to_initial_state(
+      be_verbose = true
+    )
+    # ======================================================================= #
+    # === @internal_hash
+    #
+    # The internal Hash can be used to store internal behaviour variables
+    # rather than spawn so many different instance variables.
+    #
+    # It should be defined very early in this method.
+    # ======================================================================= #
+    @internal_hash = {}
+    # ======================================================================= #
+    # === :array_rna_sequence
+    #
+    # This can be populated with sequence objects such as:
+    #
+    #   Bioroebe::Sequence.new(''.dup, :rna)
+    #
+    # ======================================================================= #
+    @internal_hash[:array_rna_sequences] = []
+    # ======================================================================= #
+    # === :array_dna_sequence
+    # ======================================================================= #
+    @internal_hash[:array_dna_sequences] = []
+    # ======================================================================= #
+    # === :the_main_sequence_is_frozen
+    # ======================================================================= #
+    @internal_hash[:the_main_sequence_is_frozen] = false
+    # ======================================================================= #
+    # === :array_palindromes
+    # ======================================================================= #
+    @internal_hash[:array_palindromes] = []
+    # ======================================================================= #
+    # === :file_dna_string_saved
+    #
+    # Where to store our DNA string by default.
+    # ======================================================================= #
+    @internal_hash[:file_dna_string_saved] = "#{log_dir?}dna_string_saved.yml"
+    # ======================================================================= #
+    # === :array_jumper_directories
+    # ======================================================================= #
+    @internal_hash[:array_jumper_directories] = []
+    # ======================================================================= #
+    # === :array_fasta
+    # ======================================================================= #
+    @internal_hash[:array_fasta] = []
+    # ======================================================================= #
+    # === analyse_the_local_dataset_on_startup
+    #
+    # If this setting is set to true then, on startup, the bioshell
+    # will report some information about the local dataset (FASTA
+    # files and pdb files).
+    # ======================================================================= #
+    @internal_hash[:analyse_the_local_dataset_on_startup] = true
+    # ======================================================================= #
+    # === search_for
+    # ======================================================================= #
+    @internal_hash[:search_for] = nil
+    # ======================================================================= #
+    # === coding_area
+    # ======================================================================= #
+    @internal_hash[:coding_area] = nil # This can keep track of the real coding area.
+    # ======================================================================= #
+    # === misc_sequence
+    # ======================================================================= #
+    @internal_hash[:misc_sequence] = nil # This can store a misc DNA or RNA sequence.
+    # ======================================================================= #
+    # === :array_sequences
+    # ======================================================================= #
+    # @internal_hash[:array_sequences] = []
+    # ======================================================================= #
+    # === :all_arguments
+    # ======================================================================= #
+    @internal_hash[:all_arguments] = []
+    # ======================================================================= #
+    # === :remaining_arguments
+    # ======================================================================= #
+    @internal_hash[:remaining_arguments] = []
+    # ======================================================================= #
+    # === :registered_actions
+    # ======================================================================= #
+    @internal_hash[:registered_actions] = ARRAY_REGISTERED_ACTIONS
+    # ======================================================================= #
+    # === :silent_startup
+    #
+    # This variable keeps track as to whether we will display a welcome
+    # message on startup or whether we will not.
+    # ======================================================================= #
+    @internal_hash[:silent_startup] = false
+    # ======================================================================= #
+    # === :create_directories_on_startup_of_the_shell
+    #
+    # If this variable is set to true then the bio-shell will create
+    # some directories on startup. The user can modify this from
+    # the commandline, though, and specifically disable it.
+    # ======================================================================= #
+    @internal_hash[:create_directories_on_startup_of_the_shell] = true
+    # ======================================================================= #
+    # === array_history
+    #
+    # This array will keep track of the input-history, aka the commands
+    # that the user has used.
+    # ======================================================================= #
+    @internal_hash[:array_history] = []
+    # ======================================================================= #
+    # === remove_last_character_if_it_is_a_question_mark
+    #
+    # If this variable is set to true then we will remove the last
+    # input character - at the least if it is a '?'.
+    # ======================================================================= #
+    @internal_hash[:remove_last_character_if_it_is_a_question_mark] = false
+    # ======================================================================= #
+    # === :first_argument
+    #
+    # This variable refers to the first argument passed into a method,
+    # from the menu.rb file.
+    # ======================================================================= #
+    @internal_hash[:first_argument] = nil
+    # ======================================================================= #
+    # === :array_aminoacid_sequence
+    #
+    # This variable should be an empty Array, aka [], initially, so that we
+    # can distinguish the case when the user has added data onto that
+    # Array.
+    # ======================================================================= #
+    @internal_hash[:array_aminoacid_sequence] = []
+    # ======================================================================= #
+    # === exit_the_shell_how
+    #
+    # The next variable has two valid modes:
+    #
+    #   :instantly
+    #   :exit_gracefully
+    #
+    # The first is the default; the second can be used if the Bioshell
+    # is embedded into another program.
+    # ======================================================================= #
+    @internal_hash[:exit_the_shell_how] = :instantly
+    # ======================================================================= #
+    # === search_for
+    #
+    # This is the sequence we wish to find, in a given nucleotide sequence.
+    # By default this will be nil.
+    # ======================================================================= #
+    @internal_hash[:search_for] = nil
+    # ======================================================================= #
+    # === show_the_leader
+    # ======================================================================= #
+    @internal_hash[:show_the_leader]  = true # Show the 5' leader.
+    # ======================================================================= #
+    # === show_the_trailer
+    # ======================================================================= #
+    @internal_hash[:show_the_trailer] = true # Show the 3' trailer.
+    # ======================================================================= #
+    # === @save_file
+    # ======================================================================= #
+    @internal_hash[:save_file] = BIOSHELL_SAVE_FILE
+    # ======================================================================= #
+    # === @use_working_directory_as_prompt
+    # ======================================================================= #
+    @internal_hash[:use_working_directory_as_prompt] = false
+    # ======================================================================= #
+    # === @debug
+    #
+    # Determine whether we will debug or whether we will not
+    # ======================================================================= #
+    @internal_hash[:debug] = SHALL_WE_DEBUG
+    # ======================================================================= #
+    # === user_input
+    # ======================================================================= #
+    @internal_hash[:user_input] = nil
+    # ======================================================================= #
+    # === prompt_to_use
+    #
+    # This variable keeps track as to which prompt is to be used.
+    # ======================================================================= #
+    @internal_hash[:prompt_to_use] = :default
+    # ======================================================================= #
+    # === :use_xsel
+    #
+    # This method will determine whether we will use the external
+    # program "xsel". By default, at the least on my home system,
+    # I prefer to make use of xsel.
+    # ======================================================================= #
+    @internal_hash[:use_xsel] = true
+    # ======================================================================= #
+    # === @mode
+    #
+    # @mode can be either :dna or :rna or :aminoacid
+    # ======================================================================= #
+    @internal_hash[:mode] = :dna
+    # ======================================================================= #
+    # === @array_these_sequences_were_chopped_away
+    #
+    # Keep an Array that can be used to keep track of which sequences
+    # were chopped away. Whenever we perform a chop-related action we
+    # will store that sequence in an Array.
+    # ======================================================================= #
+    @internal_hash[:array_these_sequences_were_chopped_away] = []
+    # ======================================================================= #
+    # === array_timer_snapshots
+    # ======================================================================= #
+    @internal_hash[:array_timer_snapshots] = [] # This Array keeps track of the time.
+    # ======================================================================= #
+    # === may_we_show_the_startup_information
+    #
+    # This variable determines whether the startup-information may be
+    # shown, on start-up of the bioshell. By default this will be true
+    # typically, but a config-variable may overrule this.
+    # ======================================================================= #
+    @internal_hash[:may_we_show_the_startup_information] = true
+    if @configuration and @configuration.respond_to? :may_we_show_the_startup_information
+      @internal_hash[:may_we_show_the_startup_information] = @configuration.may_we_show_the_startup_information
+    end
+    # ======================================================================= #
+    # === :show_nucleotide_sequence
+    # ======================================================================= #
+    @internal_hash[:show_nucleotide_sequence] = ::Bioroebe::ShowNucleotideSequence.new(
+      '', :do_not_run_yet
+    )
+    # ======================================================================= #
+    # === fasta_file
+    #
+    # This used to be a standalone @hash variable, but during the
+    # rewrite in April 2020 this was integrated into @internal_hash.
+    # ======================================================================= #
+    @internal_hash[:fasta_file] = {}
+    # ======================================================================= #
+    # === @array_all_downloads
+    # ======================================================================= #
+    @internal_hash[:array_all_downloads] = [] # Must be an Array.
+    # ======================================================================= #
+    # === @use_working_directory_as_prompt
+    # ======================================================================= #
+    @internal_hash[:use_working_directory_as_prompt] = true
+    # ======================================================================= #
+    # === :nucleotide_sequence
+    # ======================================================================= #
+    # @internal_hash[:nucleotide_sequence] = ::Bioroebe::Sequence.new
+    # ======================================================================= #
+    # === :sequence
+    #
+    # We set thesequence to a new instance of Bioroebe::Sequence next.
+    # ======================================================================= #
+    reset_string
+    # ======================================================================= #
+    # === @use_colours
+    #
+    # Let's enable the colours.
+    # ======================================================================= #
+    enable_colours(:be_quiet)
+    # ======================================================================= #
+    # === Enable the clipboard next:
+    # ======================================================================= #
+    initialize_clipboard
+    # ======================================================================= #
+    # === Setting towards a default padding
+    #
+    # Next comes left-padding, defaulting to '  '. This should come after
+    # the clipboard has been initialized, and after @internal_hash has
+    # been fully populated.
+    # ======================================================================= #
+    set_padding :default
+    set_sequence_2
+    set_sequence_3
+    set_sequence_4
+    set_sequence_5
+    set_sequence_6
+    ::Bioroebe.clear_array_colourize_this_aminoacid
+    # ======================================================================= #
+    # === Determine whether silent startup is active
+    #
+    # Next, determine whether we will show a small startup-message or
+    # whether we shall not show it. By default this should be false -
+    # but if a file called 'use_silent_startup.yml' exists then we
+    # will use that file.
+    # ======================================================================= #
+    if File.exist? FILE_USE_SILENT_STARTUP
+      dataset = YAML.load_file(FILE_USE_SILENT_STARTUP)
+      if dataset.is_a?(Hash) and dataset.has_key?('use_silent_startup')
+        @internal_hash[:silent_startup] = dataset['use_silent_startup']
+      end
+    else # else it is 
+      @internal_hash[:silent_startup] = false
+    end
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    setup_readline if use_readline?
+    perform_startup_actions # Should come before we show the welcome message or call menu().
+    show_welcome_message    # The welcome-message should come after the startup actions.
+    menu(
+      commandline_arguments?,
+      :be_quiet_if_the_input_was_not_found
+    )
+    enter_main_loop # Enter the main user-input loop here.
+  end
+
+  # ========================================================================= #
+  # === freeze_the_main_sequence
+  # ========================================================================= #
+  def freeze_the_main_sequence
+    @internal_hash[:the_main_sequence_is_frozen] = true
+  end
+
+  # ========================================================================= #
+  # === unfreeze_the_main_sequence
+  # ========================================================================= #
+  def unfreeze_the_main_sequence
+    @internal_hash[:the_main_sequence_is_frozen] = false
+  end
+
+  # ========================================================================= #
+  # === is_the_main_sequence_frozen?
+  # ========================================================================= #
+  def is_the_main_sequence_frozen?
+    @internal_hash[:the_main_sequence_is_frozen]
+  end; alias the_main_sequence_is_frozen? is_the_main_sequence_frozen? # === the_main_sequence_is_frozen?
+
+  # ========================================================================= #
+  # === leading_3_prime
+  #
+  # This is when 3' is at the start of an output.
+  # ========================================================================= #
+  def leading_3_prime
+    "3' - "
+  end; alias leading_three_prime leading_3_prime # === leading_three_prime
+       alias leading_3           leading_3_prime # === leading_3
+
+  # ========================================================================= #
+  # === report_n_start_codons
+  #
+  # Use this method to count how many ATG codons we have. We will honour
+  # the default start_codon in use.
+  #
+  # The third argument determines which reading frame is to be used. By
+  # default, the method will use the first reading frame.
+  # ========================================================================= #
+  def report_n_start_codons(
+      this_string             = string?,
+      use_this_as_start_codon = :default, # Use the proper start codon.
+      in_which_frame          = :frame1
+    )
+    case use_this_as_start_codon
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
+    when :default
+      use_this_as_start_codon = ::Bioroebe.start_codon?
+    end
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+      case yielded
+      when /^frame/
+        in_which_frame = yielded.to_sym
+      end
+    end
+    # ======================================================================= #
+    # The following can be invoked via:
+    #   n_ORF? frame1
+    # ======================================================================= #
+    case in_which_frame
+    # ======================================================================= #
+    # === :frame1
+    # ======================================================================= #
+    when :frame1
+      in_which_frame = 'frame 1'
+    # ======================================================================= #
+    # === :frame2
+    # ======================================================================= #
+    when :frame2
+      in_which_frame = 'frame 2'
+    # ======================================================================= #
+    # === :frame3
+    # ======================================================================= #
+    when :frame3
+      in_which_frame = 'frame 3'
+    end
+    n_start_codons = this_string.upcase.scan(
+      /#{use_this_as_start_codon}/
+    ).size.to_s
+    # ======================================================================= #
+    # The above is not yet in the proper frame, though.
+    # ======================================================================= #
+    trailing_message = " Initiation Codons "\
+                       "(in #{orangered(in_which_frame)}#{rev})."
+    erev "Our main string has #{sfancy(n_start_codons)}#{rev}"\
+         " #{simp(use_this_as_start_codon)}#{rev} ("\
+         "#{use_this_as_start_codon.tr('T','U')})"+
+         trailing_message
+    if coding_area? # This has been user-supplied in that case.
+      erev 'However had, only the nucleotides from position'
+      erev "#{sfancy(coding_area?.to_s.split('..').first.to_s)}#{rev}"\
+           " to position #{sfancy(coding_area?.to_s.split('..').last.to_s)}"\
+           "#{rev} will be colourized."
+    end
+  end
+
+  # ========================================================================= #
+  # === search_sequence_for_open_reading_frames
+  #
+  # Use this method to search for Open Reading Frames (i.e. "AUG" codons).
+  #
+  # Since we use Bioroebe.start_codon?, this may also default to another
+  # start codon.
+  # ========================================================================= #
+  def search_sequence_for_open_reading_frames(
+      i                    = :default,
+      use_which_frame      = :frame1,
+      use_this_start_codon = :default
+    )
+    case use_this_start_codon
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
+    when :default
+      use_this_start_codon = ::Bioroebe.start_codon?
+    end
+    case i
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
+    when :default
+      i = string?
+    end
+    i.upcase!
+    if i
+      if i.include? use_this_start_codon # This asks whether the string includes 'ATG'.
+        report_n_start_codons # Will report how many Start sequences we have.
+        e
+        erev "These can be found (and will start) at these positions"
+        erev "(later shown via red colour):#{N}#{N}"
+        copy = i.to_s.dup # Work on a copy here.
+        if use_which_frame == :frame2 # Chop off the first entry then.
+          copy[0,1] = ''
+        end
+        # =================================================================== #
+        # We will search for both ATG and AUG though, respectively the
+        # input variants given to us. If the following regex appears to
+        # be complicated to you, here is the old variant for the regex:
+        #
+        #   use_this_regex = /(ATG|AUG)/i
+        #
+        # =================================================================== #
+        array_results = []
+        array_results << Bioroebe.return_array_of_sequence_matches(copy, use_this_start_codon)
+        if use_this_start_codon.include? 'T'
+          array_results << Bioroebe.return_array_of_sequence_matches(copy, use_this_start_codon.tr('T','U'))
+        end
+        array_results.flatten!
+        array_results.compact!
+        # =================================================================== #
+        # This will hold data such as:
+        #   [16, ["ATG"]]
+        # At the least up until April 2020, before it was changed.
+        # =================================================================== #
+        return array_results
+      else
+        []
+      end
+    else
+      ewarn 'It seems as if you have not yet assigned a string.'
+      ewarn 'You could run "random" to assign a random string.'
+    end
+  end
+
+  # ========================================================================= #
+  # === report_main_sequence
+  #
+  # We will call dna_with_ends() here in this method. The argument colourize
+  # will determine whether we will colourize the DNA strand or not.
+  #
+  # Invocation examples:
+  #
+  #    report_main_sequence(::Bioroebe.start_codon?)
+  #    report_main_sequence(:start_codon) # ← is the same as the ^^^ above
+  #    report_main_sequence(:stop_codon)  # ← Colourize the stop-codons.
+  #
+  # ========================================================================= #
+  def report_main_sequence(
+      input     = dna_sequence_as_string?,
+      colourize = nil
+    )
+    case input
+    # ======================================================================= #
+    # === :stop_codon
+    # ======================================================================= #
+    when :stop_codon
+      colourize = stop_codons?
+      input     = dna_sequence_as_string?
+    end
+    original_input = input.dup
+    case colourize
+    # ======================================================================= #
+    # === :stop_codon
+    #
+    # We attempt to colourize the stop-codons via this method.
+    # ======================================================================= #
+    when :stop_codon
+      colourize = stop_codons?
+    # ======================================================================= #
+    # === :stop_codon_in_frame1
+    # ======================================================================= #
+    when :stop_codon_in_frame1,
+         :stop_codon_in_frame2,
+         :stop_codon_in_frame3
+      new_string = remove_trailing_escape_code(
+        colour_for_nucleotides(
+          ''.dup
+        ).dup
+      ).dup
+      n_stop_codons_were_found = 0
+      prepend_this = ''.dup
+      input = input.dup # Work on a copy here.
+      case colourize
+      when :stop_codon_in_frame2
+        prepend_this << input[0,1]
+        input[0,1] = ''
+      when :stop_codon_in_frame3
+        prepend_this << input[0,2]
+        input[0,2] = ''
+      end
+      new_string << prepend_this
+      scanned = input.scan(/.../) # Get a group of codons here.
+      scanned.each {|codon|
+        if is_a_stop_codon? codon
+          n_stop_codons_were_found += 1
+          new_string << colour_for_stop_codon(codon.dup).dup+
+                        remove_trailing_escape_code(
+                          colour_for_nucleotides
+                        )
+        else
+          new_string << codon.dup
+        end
+      }
+      case colourize
+      # === :stop_codon_in_frame2
+      when :stop_codon_in_frame2
+        new_string << input[-2,2]
+      # === :stop_codon_in_frame3
+      when :stop_codon_in_frame3
+        new_string << input[-1,1]
+      end
+      
+      e "#{padding?}"\
+        "#{rev}"\
+        "#{leading_five_prime}"\
+        "#{new_string}"\
+        "#{rev}"\
+        "#{trailing_three_prime}"
+      erev "#{steelblue(n_stop_codons_were_found)} #{rev}stop "\
+           "codons were found in this sequence of #{original_input.size} "\
+           "nucleotides."
+      return
+    # ======================================================================= #
+    # === :start_codon
+    # ======================================================================= #
+    when :start_codon # Instruction to use a start codon here.
+      colourize = start_codon?
+    # ======================================================================= #
+    # === :start_and_stop_codon
+    # ======================================================================= #
+    when :start_and_stop_codon
+      colourize = [start_codon?, stop_codons?]
+    end
+    # ======================================================================= #
+    # The old code was:
+    #
+    #   erev padding?+
+    #        dna_with_ends(input, colourize) { :honour_coding_area_if_it_exists } # The dna_with_ends() method can deal with Arrays.
+    #
+    # This is now mostly ported (April 2020), but the :honour_coding_area_if_it_exists
+    # is not yet ported, so the above code will remain as-is, for the time
+    # being.
+    # ======================================================================= #
+    show_nucleotide_sequence?.report_this_sequence(input) {{
+      padding_to_use: padding?,
+      colourize_this_subsequence: colourize
+    }}
+  end; alias show_main_string         report_main_sequence # === show_main_string
+       alias show_main_sequence       report_main_sequence # === show_main_sequence
+       alias show_colourized_sequence report_main_sequence # === show_colourized_sequence
+       alias show_dna_sequence        report_main_sequence # === show_dna_sequence
+       alias show_DNA_sequence        report_main_sequence # === show_DNA_sequence
+
+  # ========================================================================= #
+  # === enable_configuration
+  # ========================================================================= #
+  def enable_configuration
+    config_dir = ::Bioroebe.project_yaml_directory?+
+                 '/configuration/'
+    unless Object.const_defined?(:Roebe) and
+           Roebe.const_defined?(:Configuration)
+      begin
+        require 'roebe/configuration/class/configuration.rb'
+      rescue LoadError; end
+    end
+    if Object.const_defined?(:Roebe) and
+       Roebe.const_defined?(:Configuration)
+      # ===================================================================== #
+      # === Initialize @configuration
+      # ===================================================================== #
+      @configuration = ::Roebe::Configuration.new(config_dir, :do_not_run_yet)
+      @configuration.be_verbose if @configuration.respond_to? :be_verbose
+      @configuration.run
+    else
+      @configuration = nil
+    end
+  end
+
+  # ========================================================================= #
+  # === find_restriction_sites
+  #
+  # Call the parent method in the Bioroebe class.
+  # ========================================================================= #
+  def find_restriction_sites(i = string?)
+    i = string? if i.nil?
+    Bioroebe.restriction_sites?(i) # bl mybioruby
+  end
+
+  # ========================================================================= #
+  # === find_complementary_strand
+  #
+  # Invoke this via:
+  #
+  #    3'-ATGCCTGCC
+  #
+  # ========================================================================= #
+  def find_complementary_strand(i = dna_sequence?)
+    _ = i.strip # The original input.
+    if _.include? "3'-" and _.start_with?('3')
+      _.gsub!(/3'-/,'')
+      _.gsub!(/-5'/,'')
+      _.gsub!(/3'-/,'')
+      erev lpad?+leading_three_prime+
+           colourize_nucleotide(_, :do_not_add_anything_else)+
+           trailing_five_prime
+    end
+    result = lpad?+
+             colourize_nucleotide(
+               return_complement(i.reverse)
+             )
+    erev result
+    return result
+  end; alias show_complementary_strand find_complementary_strand # === show_complementary_strand
+
+  # ========================================================================= #
+  # === Bioroebe::Shell.menu
+  #
+  # To test this, try:
+  #
+  #   Bioroebe::Shell.menu('ll')
+  #
+  # ========================================================================= #
+  def self.menu(i = ARGV)
+    new(:no_commandline_arguments).menu(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Shell[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Shell.upload_this_pdf_file
+  #
+  # Use this method to upload the .pdf tutorial or any other .pdf
+  # file. This is primarily useful on my home system and may have
+  # very little value to other people.
+  # ========================================================================= #
+  def self.upload_this_pdf_file(path)
+    # ======================================================================= #
+    # ^^^ This will have generated the .pdf.
+    # ======================================================================= #
+    # Hardcoded for now where the .pdf will reside.
+    # ======================================================================= #
+    if Object.const_defined? :FtpParadise
+      ftp = FtpParadise.new(:shevy, :dont_run_yet)
+      ftp.do_login
+      ftp.upload_this_binary_file(path)
+      e 'Finished uploading!'
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Shell.generate_pdf_tutorial
+  #
+  # You can use this method to simply generate a new .pdf file, then
+  # upload it anyway.
+  # ========================================================================= #
+  def self.generate_pdf_tutorial(
+      also_upload_the_tutorial = true
+    )
+    url = ::Bioroebe.try_to_pass_through_beautiful_url('bioroebe_tutorial?pdf')
+    url = url.first if url.is_a? Array
+    url.gsub!(/^\/home\/x\/data\//, LOCALHOST) if url.include? HOME_DIRECTORY_OF_USER_X+'data/'
+    OpenURI.send(:open, url)
+    # ======================================================================= #
+    # === Designate where the tutorial can be found locally
+    # ======================================================================= #
+    path = FILE_BIOROEBE_TUTORIAL
+    if also_upload_the_tutorial
+      if File.exist? path
+        ::Bioroebe.upload_this_pdf_file(path)
+      else
+        e "Can not upload from #{sfile(path.to_s)} as this "\
+          "path does not exist."
+      end
+    end
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.upload_this_pdf_file
+# =========================================================================== #
+def self.upload_this_pdf_file(i)
+  ::Bioroebe::Shell.upload_this_pdf_file(i)
+end
+
 # =========================================================================== #
-# Next, batch-require all toplevel_methods/ from the bioroebe project:
-# =========================================================================== #
-require 'bioroebe/requires/require_the_toplevel_methods.rb'
-
-# =========================================================================== #
-# Next require shell-specific ruby files:
-# =========================================================================== #
-require 'bioroebe/shell/colours/colours.rb'
-require 'bioroebe/shell/help/help.rb'
-require 'bioroebe/shell/constants.rb'
-require 'bioroebe/shell/download.rb'
-require 'bioroebe/shell/enable_and_disable.rb'
-require 'bioroebe/shell/initialize.rb'
-require 'bioroebe/shell/history.rb'
-require 'bioroebe/shell/loop.rb'
-require 'bioroebe/shell/menu.rb'
-require 'bioroebe/shell/misc.rb'
-require 'bioroebe/shell/prompt.rb'
-require 'bioroebe/shell/readline/readline.rb'
-require 'bioroebe/shell/reset.rb'
-require 'bioroebe/shell/scan_and_parse.rb'
-require 'bioroebe/shell/search.rb'
-require 'bioroebe/shell/sequences.rb'
-require 'bioroebe/shell/show_report_and_display.rb'
-require 'bioroebe/shell/startup.rb'
-require 'bioroebe/shell/taxonomy.rb'
-require 'bioroebe/shell/user_input.rb'
+# === Bioroebe.generate_pdf_tutorial
+# =========================================================================== #
+def self.generate_pdf_tutorial
+  ::Bioroebe::Shell.generate_pdf_tutorial
+end
+
+# =========================================================================== #
+# === Bioroebe.shell
+#
+# This is the main method to instantiate the Shell component of the
+# Bioroebe component.
+# =========================================================================== #
+def self.shell(i = ARGV)
+  ::Bioroebe::Shell.new(i)
+end; self.instance_eval { alias start_shell shell } # === Bioroebe.start_shell
+
+end
 
 if __FILE__ == $PROGRAM_NAME
   Bioroebe::Shell.new(ARGV)
+  # Bioroebe::Shell.new.enable_gtk_section_antisensestrand
 end