bioroebe 0.10.80

data/lib/bioroebe/colours/colours.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This file will contain support for colours, through the 'colours' gem.
+#
+# The reason why this resides here is that we need a way to also modify
+# the colours for the whole Bioroebe project, that is, the main namespace
+# called Bioroebe. This is why there are topleve-level instance variables
+# such as @use_colours. Setting this variable to false will disable
+# colours for the Bioroebe project.
+# =========================================================================== #
+# require 'bioroebe/colours/colours.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/requires/require_colours.rb'
+  require 'bioroebe/colours/misc_colours.rb'
+  require 'bioroebe/colours/rev.rb'
+  require 'bioroebe/colours/sdir.rb'
+  require 'bioroebe/colours/sfancy.rb'
+  require 'bioroebe/colours/sfile.rb'
+  require 'bioroebe/colours/simp.rb'
+  require 'bioroebe/colours/swarn.rb'
+
+  # ========================================================================= #
+  # === Bioroebe::USE_THIS_COLOUR_FOR_DNA
+  #
+  # The following constant will denote which colour we will use for DNA
+  # sequences by default, in this case, the HTML colour called steelblue.
+  # ========================================================================= #
+  USE_THIS_COLOUR_FOR_DNA = :steelblue
+
+  # ========================================================================= #
+  # === @default_colour
+  #
+  # This colour is used by default.
+  # ========================================================================= #
+  @default_colour = nil
+  @default_colour = Colours::GREEN if @use_colours
+
+  # ========================================================================= #
+  # === Bioroebe.default_colour?
+  # ========================================================================= #
+  def self.default_colour?
+    @default_colour
+  end; self.instance_eval { alias main_colour default_colour? } # === Bioroebe.main_colour
+       self.instance_eval { alias main_col    default_colour? } # === Bioroebe.main_col
+
+  # ========================================================================= #
+  # === default_colour?
+  # ========================================================================= #  
+  def default_colour?
+    ::Bioroebe.default_colour?
+  end; alias main_colour default_colour? # === main_colour
+       alias main_col    default_colour? # === main_col
+
+  # ========================================================================= #
+  # === Bioroebe.set_default_colour
+  #
+  # This is primarily used by the Bioroebe::Shell.
+  # ========================================================================= # 
+  def self.set_default_colour(i)
+    @default_colour = i
+  end
+
+  # ========================================================================= #
+  # === use_colours_in_general?
+  # ========================================================================= #
+  def use_colours_in_general?
+    ::Bioroebe.use_colours?
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.colours
+  #
+  # This method can be used to quickly enable or disable colours,
+  # by passing '+' or '-'.
+  # ========================================================================= #
+  def self.colours(enable_or_disable = '+')
+    case enable_or_disable.to_s
+    when '+',
+         'true'
+      enable_colours
+    when '-',
+         'false',
+         ''
+      disable_colours
+    end
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.disable_colours
+  #
+  # Use this method if you wish to disable colours for the whole Bioroebe
+  # project.
+  # ========================================================================= #
+  def self.disable_colours(be_verbose = false)
+    if be_verbose
+      e 'Disabling colours.'
+    end
+    @use_colours = false
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.enable_colours
+  #
+  # Use this method to enable colours for the whole Bioroebe project.
+  #
+  # All classes that are part of the Bioroebe project should honour
+  # this setting (if it is a class that may make use of colours;
+  # some smaller classes do not need colours, and hence have no need
+  # for the method here).
+  # ========================================================================= #
+  def self.enable_colours
+    @use_colours = true
+  end; self.instance_eval { alias enablecolours enable_colours } # === Bioroebe.enablecolours
+
+end

data/lib/bioroebe/colours/misc_colours.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# This file contains in particular the HTML colours.
+# =========================================================================== #
+# require 'bioroebe/colours/misc_colours.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/requires/require_colours.rb'
+
+  # ========================================================================= #
+  # === HTML-colours
+  #
+  # Next we will batch-define several colours. Keep them sorted
+  # alphabetically.
+  # ========================================================================= #
+  array_colours_to_define = %w(
+    cornflowerblue
+    darkgreen
+    dodgerblue
+    gold
+    mediumorchid
+    mediumseagreen
+    mediumspringgreen
+    mediumturquoise
+    mediumvioletred
+    oldlace
+    olivedrab
+    orangered
+    orchid
+    palegoldenrod
+    palegreen
+    plum
+    rosybrown
+    royalblue
+    seagreen
+    slateblue
+    springgreen
+    steelblue
+    teal
+    tomato
+    violet
+    wheat
+    white
+    whitesmoke
+    yellow
+    yellowgreen
+  )
+
+  array_colours_to_define.each {|use_this_colour|
+    self.class.instance_eval {
+      define_method(use_this_colour.to_sym) {|i = ''|
+        return Colours.send(use_this_colour.to_sym, i) if @use_colours
+        return i
+      }
+    }
+  }
+
+  # ========================================================================= #
+  # === ecomment
+  # ========================================================================= #
+  def ecomment(i)
+    return Colours.ecomment(i) if use_colours_in_general?
+    return i
+  end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  # ========================================================================= #
+  # Some test-code comes next:
+  # ========================================================================= #
+  alias e puts
+  e Bioroebe.dodgerblue('Hello world!')
+  e Bioroebe.teal('Hello world!')
+  e Bioroebe.springgreen('Hello world!')
+  e Bioroebe.violet('Hello world!')  
+end

data/lib/bioroebe/colours/rev.rb

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+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/rev.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/colours/use_colours.rb'
+
+  # ========================================================================= #
+  # === Bioroebe.rev                                                (rev tag)
+  #
+  # The general pointer towards using the default colour.
+  #
+  # This will, however had, only be in use if we do not use colours.
+  # ========================================================================= #
+  def self.rev
+    if @use_colours
+      return Colours::GREEN # Default colour goes in here.
+    end
+    return ''
+  end
+
+  # ========================================================================= #
+  # === rev
+  #
+  # Delegate towards Bioroebe.rev() there.
+  # ========================================================================= #
+  def rev
+    ::Bioroebe.rev
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.erev
+  # ========================================================================= #
+  def self.erev(i = '')
+    puts "#{rev}#{i}"
+  end
+
+end

data/lib/bioroebe/colours/sdir.rb

@@ -0,0 +1,21 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/sdir.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/colours/use_colours.rb'
+
+  # ========================================================================= #
+  # === Bioroebe.sdir
+  # ========================================================================= #
+  def self.sdir(i = '')
+    if @use_colours
+      i = Colours.sdir(i)
+    end
+    return i
+  end
+
+end

data/lib/bioroebe/colours/sfancy.rb

@@ -0,0 +1,21 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/sfancy.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/colours/use_colours.rb'
+
+  # ========================================================================= #
+  # === Bioroebe.sfancy
+  # ========================================================================= #
+  def self.sfancy(i = '')
+    if @use_colours
+      return Colours.sfancy(i)
+    end
+    return i
+  end
+
+end

data/lib/bioroebe/colours/sfile.rb

@@ -0,0 +1,21 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/sfile.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/colours/use_colours.rb'
+
+  # ========================================================================= #
+  # === Bioroebe.sfile
+  # ========================================================================= #
+  def self.sfile(i = '')
+    if @use_colours
+      return Colours.sfile(i)
+    end
+    return i
+  end
+
+end

data/lib/bioroebe/colours/simp.rb

@@ -0,0 +1,21 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/simp.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/colours/use_colours.rb'
+
+  # ========================================================================= #
+  # === Bioroebe.simp
+  # ========================================================================= #
+  def self.simp(i = '')
+    if @use_colours
+      return Colours.simp(i)
+    end
+    return i
+  end
+
+end

data/lib/bioroebe/colours/swarn.rb

@@ -0,0 +1,29 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/swarn.rb'
+# =========================================================================== #
+module Bioroebe
+
+  require 'bioroebe/colours/use_colours.rb'
+
+  # ========================================================================= #
+  # === Bioroebe.swarn
+  # ========================================================================= #
+  def self.swarn(i = '')
+    if @use_colours
+      return Colours.swarn(i)
+    end
+    return i
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.swarn
+  # ========================================================================= #
+  def self.ewarn(i = '')
+    require 'bioroebe/toplevel_methods/e.rb'
+    e swarn(i)
+  end
+
+end

data/lib/bioroebe/colours/use_colours.rb

@@ -0,0 +1,27 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/colours/use_colours.rb'
+# =========================================================================== #
+module Bioroebe
+
+  # ========================================================================= #
+  # === @use_colours
+  #
+  # Whether the whole Bioroebe project will make use of colours or
+  # whether it will not.
+  # ========================================================================= #
+  @use_colours = true
+
+  # ========================================================================= #
+  # === Bioroebe.use_colours?
+  #
+  # Query-method to determine whether the Bioroebe gem will try to make
+  # use of colours.
+  # ========================================================================= #
+  def self.use_colours?
+    @use_colours
+  end; self.instance_eval { alias use_colours_in_general? use_colours? } # === Bioroebe.use_colours_in_general?
+
+end

data/lib/bioroebe/configuration/configuration.rb

@@ -0,0 +1,114 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/configuration/configuration.rb'
+# Bioroebe.use_opn?
+# =========================================================================== #
+module Bioroebe
+
+module Configuration # === Bioroebe::Configuration
+
+  require 'bioroebe/project/project.rb'
+  require 'bioroebe/configuration/constants.rb'
+  require 'bioroebe/toplevel_methods/is_on_roebe.rb'
+  require 'bioroebe/requires/require_yaml.rb'
+
+  # ========================================================================= #
+  # === @use_expand_cd_aliases
+  #
+  # Determine whether we will use cd-aliases or whether we will not.
+  #
+  # As of now, only on my home system will this be in use.
+  # ========================================================================= #
+  if ::Bioroebe.is_on_roebe? # On my home system.
+    @use_expand_cd_aliases = true
+  else # On other people's system.
+    @use_expand_cd_aliases = false
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Configuration.do_not_use_expand_cd_aliases
+  # ========================================================================= #
+  def self.do_not_use_expand_cd_aliases
+    @use_expand_cd_aliases = false
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Configuration.do_use_expand_cd_aliases
+  # ========================================================================= #
+  def self.do_use_expand_cd_aliases
+    @use_expand_cd_aliases = true
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Configuration.use_expand_cd_aliases?
+  #
+  # Query whether we will use class Rcfiles::DirectoryAliases or whether
+  # we will not. Boolean value.
+  # ========================================================================= #
+  def self.use_expand_cd_aliases?
+    @use_expand_cd_aliases
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Configuration.n_chunks?
+  #
+  # How many chunks to display when we translate from DNA to AA.
+  # ========================================================================= #
+  def self.n_chunks?
+    30
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::Configuration.log_user_input?
+  #
+  # If the following returns true, then we will log all user-input into
+  # a file called 'history_log.yml'.
+  # ========================================================================= #
+  def self.log_user_input?
+    true
+  end
+
+  # ========================================================================= #
+  # === Bioroebe.use_opn?
+  #
+  # Query method to determine whether we will make use of Opn.opn() or
+  # whether we will not. By default we will, but the user can overrule this
+  # via a .yml configuration file.
+  # ========================================================================= #
+  def self.use_opn?(
+      use_this_file = "#{CONFIGURATION_DIRECTORY}use_opn.yml"
+    )
+    if File.exist? use_this_file
+      YAML.load_file(use_this_file)
+    else
+      true # This is the default value in that case.
+    end
+  end
+
+end
+
+# =========================================================================== #
+# === Bioroebe.use_opn?
+#
+# This is the toplevel-method that should be used, ideally, for
+# determining whether opn will be used for the bioroebe project.
+# =========================================================================== #
+def self.use_opn?
+  ::Bioroebe::Configuration.use_opn?
+end
+
+# =========================================================================== #
+# === Bioroebe.try_to_rename_kde_konsole?
+# =========================================================================== #
+def self.try_to_rename_kde_konsole?
+  ::Bioroebe::Configuration::TRY_TO_RENAME_KDE_KONSOLE
+end
+
+end
+
+if __FILE__ == $PROGRAM_NAME
+  pp Bioroebe.try_to_rename_kde_konsole?
+  pp Bioroebe.use_opn?  
+end

data/lib/bioroebe/configuration/constants.rb

@@ -0,0 +1,35 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Configuration
+# =========================================================================== #
+# require 'bioroebe/configuration/constants.rb'
+# =========================================================================== #
+module Bioroebe
+
+module Configuration # === Bioroebe::Configuration
+
+  # ========================================================================= #
+  # === DEFAULT_EDITOR_TO_USE
+  #
+  # You can designate your main editor here; this is the default editor
+  # that is to be used whenever file-editing may be done in the
+  # BioRoebe project.
+  # ========================================================================= #
+  if ENV['IS_ROEBE']
+    DEFAULT_EDITOR_TO_USE = 'bluefish' # Could be vim too.
+  else # else assume that we may be on windows, so let's use notepad++ in this event.
+    DEFAULT_EDITOR_TO_USE = 'notepad++.exe'
+  end
+
+  # ========================================================================= #
+  # === TRY_TO_RENAME_KDE_KONSOLE
+  #
+  # If the following constant is set to true, then we will try
+  # to rename the KDE konsole on startup of the bioroebe shell,
+  # if possible.
+  # ========================================================================= #
+  TRY_TO_RENAME_KDE_KONSOLE = true
+
+end; end

data/lib/bioroebe/constants/GUIs.rb

@@ -0,0 +1,79 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI
+# =========================================================================== #
+# require 'bioroebe/constants/GUIs.rb'; include ::Bioroebe::GUI
+# =========================================================================== #
+module Bioroebe
+
+module GUI # === Bioroebe::GUI
+
+  # ========================================================================= #
+  # === ARRAY_ALL_GTK_WIDGETS
+  #
+  # List all gtk-widgets that are relevant for the controller-application.
+  # ========================================================================= #
+  ARRAY_ALL_GTK_WIDGETS = %w(
+    anti_sense_strand/anti_sense_strand.rb
+    calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb
+    dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb
+    hamming_distance/hamming_distance.rb
+    levensthein_distance/levensthein_distance.rb
+    protein_to_DNA/protein_to_DNA.rb
+    random_aminoacids/random_aminoacids.rb
+    restriction_enzymes/restriction_enzymes.rb
+    www_finder/www_finder.rb
+    dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb
+  )
+
+  # ========================================================================= #
+  # === USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS
+  #
+  # This specifies the main font that is to be used for GUI applications
+  # pertaining to Bioroebe.
+  # ========================================================================= #
+  USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS =
+    'DejaVu Sans Mono'
+
+  # ========================================================================= #
+  # === FONT_SIZE
+  #
+  # Uniform default font-size for the whole GUI part.
+  # ========================================================================= #
+  FONT_SIZE = '22'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = "#{USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS} #{FONT_SIZE}"
+
+  # ========================================================================= #
+  # === OLD_VERBOSE_VALUE
+  # ========================================================================= #
+  OLD_VERBOSE_VALUE = $VERBOSE
+
+  # ========================================================================= #
+  # === disable_warnings
+  # ========================================================================= #
+  def disable_warnings
+    $VERBOSE = nil
+  end
+
+  # ========================================================================= #
+  # === enable_warnings
+  # ========================================================================= #
+  def enable_warnings
+    $VERBOSE = OLD_VERBOSE_VALUE
+  end
+
+  require 'bioroebe/toplevel_methods/log_directory.rb'
+  # ========================================================================= #
+  # === log_dir?
+  # ========================================================================= #
+  def log_dir?
+    ::Bioroebe.log_dir?
+  end
+
+end; end