bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/{gtk3 → universal_widgets}/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb

@@ -2,70 +2,86 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::DnaToAminoacidWidget
+# === Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
-# Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
+# require 'bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb'
 # =========================================================================== #
-require 'gtk_paradise/require_gtk3'
+require 'universal_widgets/base/base.rb'
 
 module Bioroebe
 
 module GUI
 
-module Gtk
+module UniversalWidgets
 
-class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget 
+class DnaToAminoacidWidget < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
 
   require 'bioroebe/constants/GUIs.rb'
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-  require 'bioroebe/toplevel_methods/misc.rb'
+  include Bioroebe::GUI
+
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
   require 'bioroebe/codons/codons.rb'
   require 'bioroebe/codons/codon_table.rb'
   require 'bioroebe/codons/show_codon_tables.rb'
 
-  require 'gtk_paradise/requires/require_the_base_module.rb'
-  include ::Gtk::BaseModule
-
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === TITLE
+  #
+  # Specify which title to use for this small widget.
   # ========================================================================= #
   TITLE = 'DNA to Aminoacid Sequence converter'
 
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH  = '80%'
+  WIDTH = '65% or 500px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = '35% or minimum 120px'
+  HEIGHT = '55% or 300px minimum'
 
   # ========================================================================= #
-  # === MAIN_FONT
+  # === TEXT_COMPARE_THE_TWO_SEQUENCES
+  # ========================================================================= #
+  TEXT_COMPARE_THE_TWO_SEQUENCES = '_Compare the two sequences'
+
+  # ========================================================================= #
+  # === MONOSPACED_FONT
+  #
+  # When this font is changed, don't forget to also change the font
+  # at SMALLER_FONT.
   # ========================================================================= #
-  MAIN_FONT = :dejavu_condensed_16
+  MONOSPACED_FONT = :hack_20
+    USE_THIS_FONT = MONOSPACED_FONT
 
   # ========================================================================= #
   # === SMALLER_FONT
   # ========================================================================= #
-  SMALLER_FONT = :dejavu_condensed_14
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
 
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
   def initialize(
-      commandline_arguments = ARGV,
+      commandline_arguments = nil,
       run_already           = true
     )
-    super(:vertical)
+    determine_the_GUI_to_be_used(commandline_arguments)
     reset
     set_commandline_arguments(
       commandline_arguments
@@ -77,15 +93,19 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # === reset                                                     (reset tag)
   # ========================================================================= #
   def reset
+    super() if respond_to?(:super)
     reset_the_internal_variables
+    reset_the_base_module # This must come after reset_the_internal_variables().
+    infer_the_namespace
     # ======================================================================= #
     # === @configuration
     # ======================================================================= #
-    @configuration = [true, __dir__, NAMESPACE]
+    @configuration = [true, __dir__, namespace?]
+    # ======================================================================= #
+    # === Set the title, width, height and the font in use.
+    # ======================================================================= #
     title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
-    infer_the_size_automatically
-    set_border_width(15) if respond_to? :set_border_width
-    signal_destroy_then_quit
+    handle_CSS if use_gtk3?
     # ======================================================================= #
     # === @dna_sequence
     #
@@ -102,15 +122,6 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     # === @parent_widget
     # ======================================================================= #
     @parent_widget = nil
-    handle_CSS_rules
-  end
-
-  # ========================================================================= #
-  # === handle_CSS_rules
-  # ========================================================================= #
-  def handle_CSS_rules
-    use_gtk_paradise_project_css_file
-    append_project_CSS_file 
   end
 
   # ========================================================================= #
@@ -124,7 +135,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # === border_size?
   # ========================================================================= #
   def border_size?
-    4
+    8
   end
 
   # ========================================================================= #
@@ -162,20 +173,61 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   end
 
   # ========================================================================= #
-  # === dna_sequence?
+  # === set_aminoacid_sequence
   # ========================================================================= #
-  def dna_sequence?
-    left_entry?.text.to_s
-  end; alias return_the_main_DNA_sequence dna_sequence? # === return_the_main_DNA_sequence
+  def set_aminoacid_sequence(i)
+    @aminoacid_sequence = i
+  end; alias set_these_aminoacids set_aminoacid_sequence # === set_these_aminoacids
 
   # ========================================================================= #
-  # === create_the_entries                                      (entries tag)
+  # === do_the_conversion                                    (conversion tag)
+  #
+  # This is the method that is to be used for the actual conversion.
   # ========================================================================= #
-  def create_the_entries
-    create_the_left_entry
-    create_the_right_entry
-    create_the_entry_for_the_codon_table_in_use
-  end
+  def do_the_conversion(
+      i = @dna_sequence
+    )
+    # ======================================================================= #
+    # Next, we must translate from DNA to Aminoacid sequence.
+    # ======================================================================= #
+    sanitized_input = i.delete(' ').delete('-')
+    i.tr!('U','T') if i.include? 'U'
+    set_dna_sequence(i)
+    if ::Bioroebe.const_defined? :Controller
+      # ===================================================================== #
+      # Ok, in this case we can store the dataset via a class-method.
+      # ===================================================================== #
+      ::Bioroebe::GUI::Controller.set_dna_sequence(i)
+    end
+    aminoacid_sequence = ::Bioroebe.convert_dna_to_protein_sequence(
+      sanitized_input,
+      :default,
+      Bioroebe::CodonTable.by_name(
+        entry_for_the_codon_table?.text?
+      )
+    )
+    set_aminoacid_sequence(aminoacid_sequence)
+    update_the_entries
+    sync_the_entries_back_onto_the_two_main_strings
+    if @parent_widget and @parent_widget.respond_to?(:set_aminoacid_sequence)
+      @parent_widget.set_aminoacid_sequence(aminoacid_sequence)
+    end
+    @label_n_DNA_nucleotides.set_text(
+      'n DNA nucleotides: '+
+      i.delete(' ').
+        delete('-').size.to_s
+    )
+    @label_n_DNA_nucleotides.make_bold
+    @label_n_DNA_nucleotides.align_left
+    @label_n_aminoacids.set_text(
+      'n aminoacids:      '+
+      aminoacid_sequence.size.to_s
+    )
+    @label_n_aminoacids.make_bold
+    @label_n_aminoacids.align_left
+  end; alias do_sync_fields                      do_the_conversion # === do_sync_fields
+       alias do_trigger_the_conversion           do_the_conversion # === do_trigger_the_conversion
+       alias do_determine_the_aminoacid_sequence do_the_conversion # === do_determine_the_aminoacid_sequence
 
   # ========================================================================= #
   # === create_the_entry_for_the_codon_table_in_use
@@ -184,7 +236,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     # ======================================================================= #
     # === @entry_for_the_codon_table_in_use
     # ======================================================================= #
-    @entry_for_the_codon_table_in_use = gtk_entry(Bioroebe.codon_table_in_use?.to_s)
+    @entry_for_the_codon_table_in_use = create_entry(Bioroebe.codon_table_in_use?.to_s)
     @entry_for_the_codon_table_in_use.center
     @entry_for_the_codon_table_in_use.bblack2
     @entry_for_the_codon_table_in_use.bg_azure
@@ -197,8 +249,8 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # === create_the_event_box
   # ========================================================================= #
   def create_the_event_box
-    @event_box_containing_the_right_arrow = gtk_eventbox(
-      gtk_label(:arrow_right)
+    @event_box_containing_the_right_arrow = create_eventbox(
+      text(:arrow_right)
     )
     @event_box_containing_the_right_arrow.on_clicked {
       update_the_dna_sequence_then_do_the_conversion
@@ -220,13 +272,13 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   end
 
   # ========================================================================= #
-  # === create_grid                                                (grid tag)
+  # === create_the_grid                                            (grid tag)
   # ========================================================================= #
-  def create_grid
+  def create_the_grid
     # ======================================================================= #
     # === @grid
     # ======================================================================= #
-    @grid = gtk_grid
+    @grid = create_grid
     @grid.set_column_spacing(5)
     @grid.set_row_spacing(5)
   end
@@ -235,7 +287,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   # === sanitized_half_width
   # ========================================================================= #
   def sanitized_half_width
-    (@width / 2) - 30
+    (width? / 2.to_f) - 30
   end
 
   # ========================================================================= #
@@ -294,7 +346,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     # ======================================================================= #
     # === The right Aminoacid widget.
     # ======================================================================= #
-    @right_entry = gtk_entry
+    @right_entry = create_entry
     @right_entry.clear_background
     @right_entry.lightskyblue_background
     @right_entry.bblack1
@@ -308,72 +360,98 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   end
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === dna_sequence?
   # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    # ======================================================================= #
-    # The two top labels denote which widget is the one for the DNA
-    # sequence, and which one is for the aminoacid sequence.
-    # ======================================================================= #
-    dna_sequence_label       = bold_label('DNA sequence')
-    dna_sequence_label.set_size_request(sanitized_half_width, 42)
-    aminoacid_sequence_label = bold_label('Aminoacid sequence')
-    aminoacid_sequence_label.set_size_request(sanitized_half_width, 42)
-    # ======================================================================= #
-    # API for .attach() is:
-    #   .attach(child, left, top, width, height)
-    # ======================================================================= #
-    @grid.attach(dna_sequence_label,                    0, 0, 2, 1)
-    @grid.attach(aminoacid_sequence_label,              3, 0, 2, 1)
-    @grid.attach(@left_entry,                           0, 1, 2, 1)
-    @grid.attach(@event_box_containing_the_right_arrow, 2, 1, 1, 1)
-    @grid.attach(@right_entry,                          3, 1, 2, 1)
-    button_box = simplified_button_box(button_trigger_the_conversion?)
-    button_box.set_size_request(350, 40)
-    @grid.attach(
-      button_box, 0, 2, 5, 1
-    )
-    minimal(@header_bar)
-    add(horizontal_spacer)
-    minimal(@grid, 8)
-    add(horizontal_spacer)
-    hbox = gtk_hbox
+  def dna_sequence?
+    left_entry?.text.to_s
+  end; alias return_the_main_DNA_sequence dna_sequence? # === return_the_main_DNA_sequence
+
+  # ========================================================================= #
+  # === create_the_entries                                      (entries tag)
+  # ========================================================================= #
+  def create_the_entries
+    create_the_left_entry
+    create_the_right_entry
+    create_the_entry_for_the_codon_table_in_use
+  end
+
+  # ========================================================================= #
+  # === main_font?
+  # ========================================================================= #
+  def main_font?
+    USE_THIS_FONT
+  end
+
+  # ========================================================================= #
+  # === slightly_smaller_font?
+  # ========================================================================= #
+  def slightly_smaller_font?
+    USE_THIS_SLIGHTLY_SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === handle_CSS_rules                                   (CSS tag, css tag)
+  # ========================================================================= #
+  def handle_CSS_rules
+    use_gtk_paradise_project_css_file
+    append_project_css_file
+    add_these_custom_CSS_rules '
+
+#custom_treeview.view header button {
+  background-color: white;
+  color: royalblue;
+  font-weight: bold;
+  font-size: larger;
+  padding: 8px;
+}'
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    create_the_header_bar
+    create_the_grid
+    create_button_trigger_conversion
+    create_the_entries
+    create_the_event_box
+  end
+
+  # ========================================================================= #
+  # === create_button_trigger_conversion
+  # ========================================================================= #
+  def create_button_trigger_conversion
     # ======================================================================= #
-    # Add the dropdown box next; also known as the combobox.
+    # === @button_trigger_conversion
     # ======================================================================= #
-    dropdown_box = gtk_dropdown_box(
-      Bioroebe.available_codon_tables?
-    )
-    dropdown_box.use_this_font = SMALLER_FONT
-    dropdown_box.first_element_is_active
-    dropdown_box.bblack1
-    dropdown_box.pad5px
-    dropdown_box.hint = 'When a new codon table is assigned, via the '\
-      'drop-down menu, then any assigned DNA sequence will be automatically '\
-      'translated to its corresponding amino acid sequence.'
-    dropdown_box.on_changed {
-      new_text = dropdown_box.text?.to_s
-      @entry_for_the_codon_table_in_use.set_text(new_text)
-      do_determine_the_aminoacid_sequence
+    @button_trigger_conversion = bold_button('_Trigger Conversion')
+    @button_trigger_conversion.clear_background
+    @button_trigger_conversion.disallow_resizing
+    @button_trigger_conversion.set_size_request(125, 40)
+    @button_trigger_conversion.set_background_colour :whitesmoke
+    @button_trigger_conversion.on_hover(:lightgreen)
+    @button_trigger_conversion.on_clicked {
+      update_the_dna_sequence_then_do_the_conversion
+      do_properly_space_the_top_left_entry
     }
-    hbox.minimal(text('Codon table in use:'),       3)
-    hbox.minimal(@entry_for_the_codon_table_in_use, 3)
-    hbox.minimal(dropdown_box,                      3)
-    add(hbox)
-    vbox = gtk_vbox
+    @button_trigger_conversion.bblack2
     # ======================================================================= #
-    # === @label_n_DNA_nucleotides
+    # Use a tooltip as well for our button:
     # ======================================================================= #
-    @label_n_DNA_nucleotides = bold_label('n DNA nucleotides: ')
-    @label_n_DNA_nucleotides.align_left
-    @label_n_DNA_nucleotides.make_selectable
-    vbox.add(@label_n_DNA_nucleotides)
-    @label_n_aminoacids = bold_label('n aminoacids:      ')
-    @label_n_aminoacids.align_left
-    @label_n_aminoacids.make_selectable
-    vbox.add(@label_n_aminoacids)
-    minimal(vbox)
+    @button_trigger_conversion.hint = 
+      "Clicking on this button will convert from a <b>DNA</b> "\
+      "<b>sequence</b> \n(on the left hand side) to the <b>corresponding "\
+      "Aminoacid sequence</b>.\n\nMake sure you input the DNA sequence "\
+      "on the left hand side. The space character, aka ' ', will "\
+      "be ignored."
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
   end
 
   # ========================================================================= #
@@ -480,7 +558,7 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
     # ======================================================================= #
     # The left entry, a DNA widget as a gtk-entry widget.
     # ======================================================================= #
-    @left_entry = gtk_entry
+    @left_entry = create_entry
     @left_entry.clear_background
     @left_entry.yellow_background
     @left_entry.bblack1
@@ -503,112 +581,95 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   end
 
   # ========================================================================= #
-  # === set_aminoacid_sequence
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
   # ========================================================================= #
-  def set_aminoacid_sequence(i)
-    @aminoacid_sequence = i
-  end; alias set_these_aminoacids set_aminoacid_sequence # === set_these_aminoacids
+  def connect_the_skeleton
+    abort_on_exception
+
+    vbox = create_vbox
 
-  # ========================================================================= #
-  # === do_the_conversion                                    (conversion tag)
-  #
-  # This is the method that is to be used for the actual conversion.
-  # ========================================================================= #
-  def do_the_conversion(
-      i = @dna_sequence
-    )
     # ======================================================================= #
-    # Next, we must translate from DNA to Aminoacid sequence.
+    # The two top labels denote which widget is the one for the DNA
+    # sequence, and which one is for the aminoacid sequence.
     # ======================================================================= #
-    sanitized_input = i.delete(' ').delete('-')
-    i.tr!('U','T') if i.include? 'U'
-    set_dna_sequence(i)
-    if ::Bioroebe.const_defined? :Controller
-      # ===================================================================== #
-      # Ok, in this case we can store the dataset via a class-method.
-      # ===================================================================== #
-      ::Bioroebe::GUI::Controller.set_dna_sequence(i)
-    end
-    aminoacid_sequence = ::Bioroebe.convert_dna_to_protein_sequence(
-      sanitized_input,
-      :default,
-      Bioroebe::CodonTable.by_name(
-        entry_for_the_codon_table?.text?
-      )
-    )
-    set_aminoacid_sequence(aminoacid_sequence)
-    update_the_entries
-    sync_the_entries_back_onto_the_two_main_strings
-    if @parent_widget and @parent_widget.respond_to?(:set_aminoacid_sequence)
-      @parent_widget.set_aminoacid_sequence(aminoacid_sequence)
-    end
-    @label_n_DNA_nucleotides.set_text(
-      'n DNA nucleotides: '+
-      i.delete(' ').
-        delete('-').size.to_s
-    )
-    @label_n_DNA_nucleotides.make_bold
-    @label_n_DNA_nucleotides.align_left
-    @label_n_aminoacids.set_text(
-      'n aminoacids:      '+
-      aminoacid_sequence.size.to_s
+    dna_sequence_label       = bold_label('DNA sequence')
+    dna_sequence_label.set_size_request(sanitized_half_width, 42)
+    aminoacid_sequence_label = bold_label('Aminoacid sequence')
+    aminoacid_sequence_label.set_size_request(sanitized_half_width, 42)
+    # ======================================================================= #
+    # API for .attach() is:
+    #   .attach(child, left, top, width, height)
+    # ======================================================================= #
+    @grid.attach(dna_sequence_label,                    0, 0, 2, 1)
+    @grid.attach(aminoacid_sequence_label,              3, 0, 2, 1)
+    @grid.attach(@left_entry,                           0, 1, 2, 1)
+    @grid.attach(@event_box_containing_the_right_arrow, 2, 1, 1, 1)
+    @grid.attach(@right_entry,                          3, 1, 2, 1)
+    button_box = simplified_button_box(button_trigger_the_conversion?)
+    button_box.set_size_request(350, 40)
+    @grid.attach(
+      button_box, 0, 2, 5, 1
     )
-    @label_n_aminoacids.make_bold
-    @label_n_aminoacids.align_left
-  end; alias do_sync_fields                      do_the_conversion # === do_sync_fields
-       alias do_trigger_the_conversion           do_the_conversion # === do_trigger_the_conversion
-       alias do_determine_the_aminoacid_sequence do_the_conversion # === do_determine_the_aminoacid_sequence
-
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    create_the_header_bar
-    create_grid
-    create_button_trigger_conversion
-    create_the_entries
-    create_the_event_box
-  end
-
-  # ========================================================================= #
-  # === create_button_trigger_conversion
-  # ========================================================================= #
-  def create_button_trigger_conversion
+    vbox.minimal(@header_bar)
+    vbox.add(horizontal_spacer)
+    vbox.minimal(@grid, 8)
+    vbox.add(horizontal_spacer)
+    hbox = create_hbox
     # ======================================================================= #
-    # === @button_trigger_conversion
+    # Add the dropdown box next; also known as the combobox.
     # ======================================================================= #
-    @button_trigger_conversion = bold_button('_Trigger Conversion')
-    @button_trigger_conversion.clear_background
-    @button_trigger_conversion.disallow_resizing
-    @button_trigger_conversion.set_size_request(125, 40)
-    @button_trigger_conversion.set_background_colour :whitesmoke
-    @button_trigger_conversion.on_hover(:lightgreen)
-    @button_trigger_conversion.on_clicked {
-      update_the_dna_sequence_then_do_the_conversion
-      do_properly_space_the_top_left_entry
+    dropdown_box = gtk_dropdown_box(
+      Bioroebe.available_codon_tables?
+    )
+    dropdown_box.use_this_font = SMALLER_FONT
+    dropdown_box.first_element_is_active
+    dropdown_box.bblack1
+    dropdown_box.pad5px
+    dropdown_box.hint = 'When a new codon table is assigned, via the '\
+      'drop-down menu, then any assigned DNA sequence will be automatically '\
+      'translated to its corresponding amino acid sequence.'
+    dropdown_box.on_changed {
+      new_text = dropdown_box.text?.to_s
+      @entry_for_the_codon_table_in_use.set_text(new_text)
+      do_determine_the_aminoacid_sequence
     }
-    @button_trigger_conversion.bblack2
+    hbox.minimal(text('Codon table in use:'),       3)
+    hbox.minimal(@entry_for_the_codon_table_in_use, 3)
+    hbox.minimal(dropdown_box,                      3)
+    vbox.add(hbox)
+    
     # ======================================================================= #
-    # Use a tooltip as well for our button:
+    # === @label_n_DNA_nucleotides
     # ======================================================================= #
-    @button_trigger_conversion.hint = 
-      "Clicking on this button will convert from a <b>DNA</b> "\
-      "<b>sequence</b> \n(on the left hand side) to the <b>corresponding "\
-      "Aminoacid sequence</b>.\n\nMake sure you input the DNA sequence "\
-      "on the left hand side. The space character, aka ' ', will "\
-      "be ignored."
-  end
+    @label_n_DNA_nucleotides = bold_label('n DNA nucleotides: ')
+    @label_n_DNA_nucleotides.align_left
+    @label_n_DNA_nucleotides.make_selectable
+    vbox.add(@label_n_DNA_nucleotides)
+    @label_n_aminoacids = bold_label('n aminoacids:      ')
+    @label_n_aminoacids.align_left
+    @label_n_aminoacids.make_selectable
+    vbox.add(@label_n_aminoacids)
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << vbox
 
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    super()
     menu
+
+    ::UniversalWidgets.set_main_window(window)
+    upon_delete_event_quit_the_application
+    window.use_this_font = font?
+    window.show_all
+    window.set_size_request(width?, height?)
+    window.set_default_size(width?, height?)
+    window.set_padding(padding?)
+    window.set_border_size(border_size?)
+    window.set_size_request(80, 100)
+    window.top_left
+    run_main
   end
 
   # ========================================================================= #
-  # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget[]
+  # === Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget[]
   # ========================================================================= #
   def self.[](i = ARGV)
     new(i)
@@ -620,15 +681,16 @@ class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacid
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::DnaToAminoacidWidget.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_top_left_then_run
-  end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run_gtk3_widget
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::DnaToAminoacidWidget.new(i)
+    )
+    r.modify_background(:normal, :mintcream)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
-end # gtkdnatoaminoacidwidget
+  Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget.new(ARGV)
+end # gtkproteintodna