bioroebe 0.10.80

data/lib/bioroebe/base/colours_for_base/colours_for_base.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/colours_for_base/colours_for_base.rb'
+# include ::Bioroebe::ColoursForBase
+# =========================================================================== #
+module Bioroebe
+
+module ColoursForBase # === Bioroebe::ColoursForBase
+
+  require 'bioroebe/colours/colours.rb'
+  require 'bioroebe/colours/rev.rb'
+  require 'bioroebe/toplevel_methods/e.rb'
+
+  # ========================================================================= #
+  # === ARRAY_HTML_COLOURS_IN_USE
+  #
+  # Next, we will define the KONSOLE Colours:
+  # ========================================================================= #
+  ARRAY_HTML_COLOURS_IN_USE = %w(
+    burlywood
+    cadetblue
+    crimson
+    cyan
+    darkgreen
+    darkolivegreen
+    deepskyblue
+    forestgreen
+    gold
+    green
+    lightblue
+    lightgreen
+    lightslategray
+    lightsteelblue
+    mediumslateblue
+    mediumvioletred
+    mediumturquoise
+    mediumspringgreen
+    olivedrab
+    orangered
+    olive
+    orange
+    orchid
+    palevioletred
+    palegoldenrod
+    powderblue
+    plum
+    rosybrown
+    royalblue
+    salmon
+    seagreen
+    skyblue
+    slateblue
+    slategrey
+    springgreen
+    steelblue
+    tomato
+    mediumorchid
+    mediumpurple
+    mediumseagreen
+    paleturquoise
+    palegreen
+    peru
+    sienna
+    teal
+    turquoise
+    violet
+    yellow
+    yellowgreen
+  )
+
+  # ========================================================================= #
+  # === use_colours_within_the_bioroebe_namespace?
+  #
+  # Query whether we use colours in the whole Bioroebe namespace.
+  # ========================================================================= #
+  def use_colours_within_the_bioroebe_namespace?
+    ::Bioroebe.use_colours?
+  end
+
+  # ========================================================================= #
+  # === set_use_colours
+  # ========================================================================= #
+  def set_use_colours(i)
+    @use_colours = i
+  end
+
+  # ========================================================================= #
+  # === use_colours?
+  # ========================================================================= #
+  def use_colours?
+    @use_colours
+  end
+
+  # ========================================================================= #
+  # === egold
+  # ========================================================================= #
+  def egold(i = '')
+    i = ::Bioroebe.gold(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    e "#{i}#{rev}"
+  end
+
+  # ========================================================================= #
+  # === eorange
+  # ========================================================================= #
+  def eorange(i = '')
+    i = ::Bioroebe.orange(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    e "#{i}#{rev}"
+  end
+
+  # ========================================================================= #
+  # === colourize_this_aminoacid_sequence_for_the_commandline
+  # ========================================================================= #
+  def colourize_this_aminoacid_sequence_for_the_commandline(i)
+    ::Bioroebe.colourize_this_aminoacid_sequence_for_the_commandline(i)
+  end; alias colourize_this_aminoacid_sequence colourize_this_aminoacid_sequence_for_the_commandline # === colourize_this_aminoacid_sequence
+
+  # ========================================================================= #
+  # === KDE colours
+  #
+  # Define the KDE colours in use next.
+  # ========================================================================= #
+  ARRAY_HTML_COLOURS_IN_USE.each {|this_colour|
+    define_method(this_colour.to_sym) {|i = ''|
+      if use_colours? and use_colours_within_the_bioroebe_namespace?
+        return Colours.send(this_colour.to_sym, i)
+      end
+      i
+    }
+  }
+
+  # ========================================================================= #
+  # === return_colour_for_nucleotides
+  # ========================================================================= #
+  def return_colour_for_nucleotides
+    _ = ::Colours.send(USE_THIS_COLOUR_FOR_DNA)
+    remove_trailing_escape_part(_)
+  end
+
+  # ========================================================================= #
+  # === disable_colours
+  #
+  # If colours-support should be disabled then this method ought to
+  # be called.
+  # ========================================================================= #
+  def disable_colours
+    @use_colours = false
+  end
+
+  # ========================================================================= #
+  # === rev
+  # ========================================================================= #
+  def rev
+    if @use_colours
+      ::Bioroebe.rev # Pointer towards Bioroebe.rev
+    else
+      ''
+    end
+  end; alias rev? rev # === rev?
+
+  # ========================================================================= #
+  # === erev
+  # ========================================================================= #
+  def erev(i = '')
+    if @use_colours
+      ::Bioroebe.erev(i)
+    else
+      ::Bioroebe.e i
+    end
+  end
+
+  # ========================================================================= #
+  # === remove_trailing_escape_part
+  #
+  # This method will remove the "closing tag" from Colour-escape codes.
+  # ========================================================================= #
+  def remove_trailing_escape_part(i)
+    ::Colours.remove_trailing_end_from(i)
+  end; alias remove_trailing_escape_code remove_trailing_escape_part # === remove_trailing_escape_code
+       alias remove_escape_sequence      remove_trailing_escape_part # === remove_escape_sequence
+       alias remove_escape_sequences     remove_trailing_escape_part # === remove_escape_sequences
+
+  # ========================================================================= #
+  # === colourize_this_nucleotide_sequence
+  #
+  # This method will colourize the given input-sequence.
+  #
+  # Note that for strings that contain escape-codes it is better to
+  # first sanitize these strings, and remove these escape codes,
+  # before proceeding with this method here.
+  # ========================================================================= #
+  def colourize_this_nucleotide_sequence(
+      i, use_colours = @use_colours
+    )
+    if use_colours
+      return return_colour_for_nucleotides+
+             i+
+             return_colour_for_nucleotides
+    end
+    return i
+  end; alias colourize_dna colourize_this_nucleotide_sequence # === colourize_dna
+
+  # ========================================================================= #
+  # === sdir
+  # ========================================================================= #
+  def sdir(i = '')
+    return Colours.sdir(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
+  # ========================================================================= #
+  # === sfancy
+  # ========================================================================= #
+  def sfancy(i = '')
+    return powderblue(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
+  # ========================================================================= #
+  # === simp
+  # ========================================================================= #
+  def simp(i = '')
+    return ::Bioroebe.simp(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    return i
+  end; alias simportant simp # === simportant
+
+  # ========================================================================= #
+  # === swarn
+  # ========================================================================= #
+  def swarn(i = '')
+    return Colours.swarn(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
+  # ========================================================================= #
+  # === eparse
+  # ========================================================================= #
+  def eparse(i)
+    return ::Colours.eparse(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
+  # ========================================================================= #
+  # === sfile
+  # ========================================================================= #
+  def sfile(i)
+    return ::Bioroebe.sfile(i) if use_colours? and use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
+  # ========================================================================= #
+  # === ecomment
+  # ========================================================================= #
+  def ecomment(i)
+    return ::Colours.ecomment(i) if use_colours?
+    return i
+  end
+
+  # ========================================================================= #
+  # === red
+  # ========================================================================= #
+  def red(i)
+    return swarn(i) if use_colours_within_the_bioroebe_namespace?
+    return i
+  end
+
+  # ========================================================================= #
+  # === enable_colours
+  # ========================================================================= #
+  def enable_colours
+    @use_colours = true
+  end
+
+end; end

data/lib/bioroebe/base/commandline_application/README.md

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+This directory will contain code for all commandline-applications
+that are part of the Bioroebe project.
+
+To subclass from this class do:
+
+  require 'bioroebe/base/commandline_application/commandline_application.rb'
+  < ::Bioroebe::CommandlineApplication

data/lib/bioroebe/base/commandline_application/aminoacids.rb

@@ -0,0 +1,33 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/commandline_application/aminoacids.rb'
+# =========================================================================== #
+module Bioroebe
+
+class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
+
+  # ========================================================================= #
+  # === return_array_of_one_letter_aminoacids
+  #
+  # This method will return a sorted Array of the one-letter aminoacids.
+  #
+  # Specifically, this may look like this:
+  #
+  #   ["A","C","D","E","F","G","H","I","K","L","M","N",
+  #    "O","P","Q","R","S","T","U","V","W","Y"]
+  #
+  # ========================================================================= #
+  def return_array_of_one_letter_aminoacids
+    AMINO_ACIDS_LONG_NAME_TO_ONE_LETTER.values.sort
+  end
+
+  # ========================================================================= #
+  # === all_aminoacids?
+  # ========================================================================= #
+  def all_aminoacids?
+    ::Bioroebe.all_aminoacids?
+  end
+
+end; end

data/lib/bioroebe/base/commandline_application/commandline_application.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/commandline_application/commandline_application.rb'
+# < ::Bioroebe::CommandlineApplication
+# =========================================================================== #
+require 'bioroebe/base/colours.rb'
+require 'bioroebe/base/prototype/prototype.rb'
+require 'bioroebe/base/misc.rb' # ← This file contains the is_palindrome? check.
+require 'bioroebe/base/commandline_application/aminoacids.rb'
+require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+require 'bioroebe/base/commandline_application/directory.rb'
+require 'bioroebe/base/commandline_application/extract.rb'
+require 'bioroebe/base/commandline_application/misc.rb'
+require 'bioroebe/base/commandline_application/opn.rb'
+require 'bioroebe/base/commandline_application/reset.rb'
+require 'bioroebe/base/commandline_application/warnings.rb'
+require 'bioroebe/base/commandline_application/write_what_into.rb'
+
+module Bioroebe
+
+class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
+
+  require 'bioroebe/constants/nucleotides.rb'
+  require 'bioroebe/constants/misc.rb'
+  require 'bioroebe/constants/urls.rb'
+
+  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/toplevel_methods/cliner.rb'
+  require 'bioroebe/toplevel_methods/log_directory.rb'
+  require 'bioroebe/toplevel_methods/open_reading_frames.rb'
+
+  include Bioroebe::ColoursForBase
+  include Bioroebe::CommandlineArguments
+
+end; end

data/lib/bioroebe/base/commandline_application/commandline_arguments.rb

@@ -0,0 +1,144 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+# include Bioroebe::CommandlineArguments
+# =========================================================================== #
+module Bioroebe
+
+module CommandlineArguments # === Bioroebe::CommandlineApplication
+
+  require 'bioroebe/base/colours_for_base/colours_for_base.rb'
+  include ::Bioroebe::ColoursForBase # Added as of 02.06.2022.
+
+  # ========================================================================= #
+  # === e
+  # ========================================================================= #
+  def e(i = '')
+    puts i
+  end
+
+  # ========================================================================= #
+  # === set_commandline_arguments
+  #
+  # This method can be used to set the commandline arguments, which
+  # usually refers to ARGV.
+  # ========================================================================= #
+  def set_commandline_arguments(i = ARGV)
+    i = [i].flatten.compact
+    @commandline_arguments = i
+  end
+
+  # ========================================================================= #
+  # === commandline_arguments?
+  #
+  # Query method to obtain all commandline arguments given to this class.
+  # ========================================================================= #
+  def commandline_arguments?
+    @commandline_arguments
+  end
+
+  # ========================================================================= #
+  # === first?
+  # ========================================================================= #
+  def first?
+    @commandline_arguments.first
+  end; alias first_argument?             first? # === first_argument?
+       alias first_argument              first? # === first_argument
+       alias input_file?                 first? # === input_file?
+       alias first_commandline_argument? first? # === first_commandline_argument?
+
+  # ========================================================================= #
+  # === commandline_arguments_that_are_files?
+  #
+  # This method will select the entries that are a file (which must
+  # exist locally).
+  # ========================================================================= #
+  def commandline_arguments_that_are_files?
+    @commandline_arguments.select {|entry| File.file?(entry.to_s) }
+  end
+
+  # ========================================================================= #
+  # === return_commandline_arguments_that_are_not_files
+  #
+  # This method will grab all entries that are NOT files.
+  # ========================================================================= #
+  def return_commandline_arguments_that_are_not_files
+    @commandline_arguments.reject {|entry| File.file?(entry.to_s) }
+  end
+
+  # ========================================================================= #
+  # === return_entries_without_two_leading_hyphens
+  #
+  # This variant will return all entries WITHOUT leading hyphens.
+  # ========================================================================= #
+  def return_entries_without_two_leading_hyphens(
+      i = @commandline_arguments
+    )
+    i.reject {|entry| entry.start_with? '--' }
+  end; alias return_commandline_arguments_without_hyphen return_entries_without_two_leading_hyphens # === return_commandline_arguments_without_hyphen
+
+  # ========================================================================= #
+  # === select_commandline_arguments
+  #
+  # This method can be used to select commandline arguments that begin
+  # with -- hyphens.
+  # ========================================================================= #
+  def select_commandline_arguments(
+      i = @commandline_arguments
+    )
+    i.select {|entry|
+      entry.start_with? '--'
+    }
+  end; alias return_commandline_arguments_starting_with_hyphens select_commandline_arguments # === return_commandline_arguments_starting_with_hyphens
+
+  # ========================================================================= #
+  # === remove_hyphens_from_the_commandline_arguments
+  # ========================================================================= #
+  def remove_hyphens_from_the_commandline_arguments(
+      i = @commandline_arguments
+    )
+    i.reject! {|entry| entry.start_with? '--' }
+  end; alias remove_hyphens_from remove_hyphens_from_the_commandline_arguments # === remove_hyphens_from
+
+  # ========================================================================= #
+  # === return_commandline_arguments_as_string
+  #
+  # This method will return the commandline arguments as a String.
+  # ========================================================================= #
+  def return_commandline_arguments_as_string
+    @commandline_arguments.join(' ').strip
+  end
+
+  # ========================================================================= #
+  # === select_entries_starting_with_two_hyphens
+  #
+  # This entry can, specifically, be used to filter out proper
+  # commandline arguments from an Array (such as ARGV).
+  # ========================================================================= #
+  def select_entries_starting_with_two_hyphens(
+      i = commandline_arguments?
+    )
+    if i.respond_to? :select
+      i.select {|entry| entry.to_s.start_with? '--' } # .to_s to prevent Integers passed.
+    else
+      []
+    end
+  end; alias commandline_arguments_with_two_leading_hyphens         select_entries_starting_with_two_hyphens # === commandline_arguments_with_two_leading_hyphens
+       alias commandline_arguments_containing_hyphens?              select_entries_starting_with_two_hyphens # === commandline_arguments_containing_hyphens?
+       alias return_entries_with_two_leading_hyphens_from           select_entries_starting_with_two_hyphens # === return_entries_with_two_leading_hyphens_from
+       alias return_arguments_with_leading_hyphens                  select_entries_starting_with_two_hyphens # === return_arguments_with_leading_hyphens
+       alias return_commandline_arguments_starting_with_hyphens     select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_hyphens
+       alias return_commandline_arguments_starting_with_two_hyphens select_entries_starting_with_two_hyphens # === return_commandline_arguments_starting_with_two_hyphens
+       alias select_two_hyphens_from                                select_entries_starting_with_two_hyphens # === select_two_hyphens_from
+       alias commandline_arguments_starting_with_leading_hyphens?   select_entries_starting_with_two_hyphens # === commandline_arguments_starting_with_leading_hyphens?
+
+  # ========================================================================= #
+  # === first_non_hyphen_argument?
+  # ========================================================================= #
+  def first_non_hyphen_argument?
+    return_entries_without_two_leading_hyphens.first
+  end; alias first_non_hyphened_argument? first_non_hyphen_argument? # === first_non_hyphened_argument?
+
+end; end

data/lib/bioroebe/base/commandline_application/directory.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/commandline_application/directory.rb'
+# =========================================================================== #
+module Bioroebe
+
+class CommandlineApplication < Base
+
+  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+  # ========================================================================= #
+  # === change_directory                                             (cd tag)
+  #
+  # Use this to change the directory. The first argument should be the
+  # target directory in question.
+  #
+  # The second argument means that this method will be verbose.
+  # ========================================================================= #
+  def change_directory(
+      i = '$HOME'
+    )
+    # ======================================================================= #
+    # The verbose-flag set next is used to also report the current directory.
+    # ======================================================================= #
+    case i
+    when ':home', :home
+      i = :home_directory
+    end
+    ::Bioroebe.change_directory(i, :be_verbose)
+  end; alias cd change_directory # === cd
+
+end; end

data/lib/bioroebe/base/commandline_application/extract.rb

@@ -0,0 +1,22 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/base/commandline_application/extract.rb' 
+# =========================================================================== #
+module Bioroebe
+
+class CommandlineApplication < Base # === Bioroebe::CommandlineApplication
+
+  # ========================================================================= #
+  # === extract                                                 (extract tag)
+  #
+  # This method can be used to extract an archive, via a hardcoded
+  # call to "tar".
+  # ========================================================================= #
+  def extract(i)
+    require 'bioroebe/toplevel_methods/extract.rb'
+    ::Bioroebe.extract(i)
+  end
+
+end; end