bioroebe 0.12.24 → 0.13.31

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

@@ -2,58 +2,82 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::AminoacidComposition
+# === Bioroebe::GUI::UniversalWidgets::AminoacidComposition
+#
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::AminoacidComposition.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
-# Bioroebe::GUI::Gtk::AminoacidComposition.run
+# require 'bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb'
 # =========================================================================== #
-require 'gtk_paradise/require_gtk3'
+require 'universal_widgets/base/base.rb'
 
 module Bioroebe
 
 module GUI
 
-module Gtk
+module UniversalWidgets
 
-class AminoacidComposition < ::Gtk::Box # === Bioroebe::GUI::Gtk::AminoacidComposition
+class AminoacidComposition < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::AminoacidComposition
 
-  require 'bioroebe/count/count_amount_of_aminoacids.rb'
-  require 'bioroebe/toplevel_methods/log_directory.rb'
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
 
-  require 'gtk_paradise/requires/require_the_base_module.rb'
-  include ::Gtk::BaseModule
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
 
-  require 'bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb'
-  include Bioroebe::GUI::AminoacidCompositionModule
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/sequence/alignment.rb'
+  require 'bioroebe/count/count_amount_of_aminoacids.rb'
+  require 'bioroebe/log_directory/log_directory.rb'
 
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Aminoacid Composition'
+  
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH = '60%'
+  WIDTH = '65% or 500px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = '40%'
+  HEIGHT = '55% or 300px minimum'
 
   # ========================================================================= #
   # === USE_THIS_FONT
   # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_18
+  USE_THIS_FONT = :hack_26
 
   # ========================================================================= #
   # === USE_THIS_SLIGHTLY_SMALLER_FONT
   # ========================================================================= #
-  USE_THIS_SLIGHTLY_SMALLER_FONT = :dejavu_condensed_16
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === FONT_FOR_THE_ENTRIES
+  #
+  # The entries must use a mono-spaced font.
+  # ========================================================================= #
+  FONT_FOR_THE_ENTRIES = :hack_22
+
+  # ========================================================================= #
+  # === FILE_MOLECULAR_WEIGHT
+  # ========================================================================= #
+  FILE_MOLECULAR_WEIGHT = Bioroebe.file_molecular_weight
 
   # ========================================================================= #
   # === 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
@@ -65,102 +89,72 @@ class AminoacidComposition < ::Gtk::Box # === Bioroebe::GUI::Gtk::AminoacidCompo
   # === 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?]
+    # ======================================================================= #
+    # === Set the title, width, height and the font in use.
+    # ======================================================================= #
     title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
-    handle_CSS_rules
-    infer_the_size_automatically
-  end
-
-  # ========================================================================= #
-  # === padding?
-  # ========================================================================= #
-  def padding?
-    6
-  end
-
-  # ========================================================================= #
-  # === border_size?
-  # ========================================================================= #
-  def border_size?
-    2
+    handle_CSS if use_gtk3?
   end
 
   # ========================================================================= #
-  # === create_skeleton                                          (create tag)
+  # === calculated_weight?
+  #
+  # This method will calculate the weight.
   # ========================================================================= #
-  def create_skeleton
-    create_user_input
-  end
-
-  # ========================================================================= #
-  # === create_user_input
-  # ========================================================================= #
-  def create_user_input
+  def calculated_weight?(i)
+    dataset = YAML.load_file(FILE_MOLECULAR_WEIGHT)
+    weight = 0
+    if i.is_a?(String) and !i.empty?
+      chars = i.chars.sort
+      chars.each {|this_char|
+        value = dataset[this_char]
+        weight += value if value
+      }
+    end
     # ======================================================================= #
-    # === @entry_input_sequence
+    # Must deduct water too.
     # ======================================================================= #
-    @entry_input_sequence = gtk_entry
-    @entry_input_sequence.hint =
-      "Input your aminoacid sequence here, then hit the enter-key to "\
-      "evaluate the given input. Invalid entries (aka <b>non-aminoacids</b>) "\
-      "will be filtered away, so do not be surprised if the sequence may "\
-      "be modified (== <b>sanitized</b>).\n\n"\
-      "The cursor-position will indicate at which aminoacid "\
-      "position we are at.\n"
-    @entry_input_sequence.yellow_background
-    @entry_input_sequence.css_class('pad4px')
-    @entry_input_sequence.signal_connect(:event) {|widget, event|
-      if is_mouse_button_release_event?(event)
-        update_information_deduced_from_the_aminoacid_sequence
-      end
-    }
+    weight -= (18.0 * (i.size - 1))
+    return weight.round(2)
   end
 
   # ========================================================================= #
-  # === set_parent_widget
+  # === update_label_cursor_position
   # ========================================================================= #
-  def set_parent_widget(i)
-    @parent_widget = i
+  def update_label_cursor_position
+    cursor_position = @entry_input_sequence.cursor_position
+    character = @entry_input_sequence.text?[cursor_position, 1].to_s
+    unless character.empty?
+      _ = 'The aminoacid at position <b>'+
+          (cursor_position+1).to_s+
+          '</b> is: <b>'+character.to_s+'</b>.'
+      @label_cursor_position.set_text(_)
+      @label_cursor_position.do_markify
+    end
   end
 
   # ========================================================================= #
-  # === fill_the_table_data_with_this_sequence
+  # === filter_away_invalid_aminoacids
   # ========================================================================= #
-  def fill_the_table_data_with_this_sequence(
-      i = @entry_input_sequence.text?
-    )
-    @list_store.clear
-    hash = Bioroebe.return_composition_from_this_aminoacid_sequence(i)
-    array = hash.to_a.map {|inner_array| inner_array.map {|entry| entry.to_s }}
-    ::Gtk.populate_this_liststore(@list_store, array)
-  end; alias fill_with_this fill_the_table_data_with_this_sequence # === fill_with_this
+  def filter_away_invalid_aminoacids(i)
+    ::Bioroebe.filter_away_invalid_aminoacids(i)
+  end
 
   # ========================================================================= #
-  # === menu                                                       (menu tag)
+  # === return_how_many_aminoacids_are_in_the_sequence
   # ========================================================================= #
-  def menu(
-      i = commandline_arguments?
+  def return_how_many_aminoacids_are_in_the_sequence(
+      i = @entry_user_input
     )
-    if i.is_a? Array
-      i.each {|entry| menu(entry) }
-    else
-      case i
-      # ===================================================================== #
-      # === gtk_aminoacid_composition --ubi
-      # ===================================================================== #
-      when /^-?-?ubiquitin$/i,
-           /^-?-?ubi$/i
-        set_main_entry(
-          Bioroebe.return_ubiquitin_sequence
-        )
-        simulate_enter_click
-      end
-    end
+    return 'This sequence has '+i.text?.to_s.size.to_s+' aminoacids.'
   end
 
   # ========================================================================= #
@@ -206,14 +200,149 @@ class AminoacidComposition < ::Gtk::Box # === Bioroebe::GUI::Gtk::AminoacidCompo
   font-size: larger;
   padding: 8px;
 }'
-    apply_the_CSS
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === return_the_first_row
+  # ========================================================================= #
+  def return_the_first_row
+    _ = create_hbox
+    top_label = left_aligned_label(
+      TEXT_INPUT_THE_SEQUENCES
+    )
+    top_label.make_selectable
+    top_label.center
+    _.minimal(top_label)
+    use_this_image = image_document_open
+    if use_this_image
+      event_box = event_box(use_this_image)
+      if event_box
+        event_box.hint = 'Click on this icon to open a local file.'
+        event_box.on_clicked {
+          do_open_and_assign_a_local_file
+        }
+        _.pack_end(event_box)
+      end
+    end
+    return _
+  end
+
+  # ========================================================================= #
+  # === create_the_text_buffer_and_the_text_view
+  # ========================================================================= #
+  def create_the_text_buffer_and_the_text_view
+    # ======================================================================= #
+    # === @text_buffer
+    # ======================================================================= #
+    @text_buffer = create_text_buffer
+    # ======================================================================= #
+    # === @text_view
+    # ======================================================================= #
+    @text_view = create_text_view(@text_buffer)
   end
 
+  # ========================================================================= #
+  # === textview?
+  # ========================================================================= #
+  def textview?
+    @text_view
+  end
+
+  # ========================================================================= #
+  # === create_the_scrolled_window
+  # ========================================================================= #
+  def create_the_scrolled_window
+    # ======================================================================= #
+    # === @scrolled_window
+    # ======================================================================= #
+    @scrolled_window = create_scrolled_window(@text_view)
+    @scrolled_window.width_height(300, 400)
+    @scrolled_window.pad4px
+    @scrolled_window.bblack2
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    6
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  end
+
+  # ========================================================================= #
+  # === smaller_font?
+  # ========================================================================= #
+  def smaller_font?
+    SMALLER_FONT
+  end
+  # ========================================================================= #
+  # === do_the_calculation
+  #
+  # This method will do the actual calculation part.
+  # ========================================================================= #
+  def do_the_calculation
+    result = ::Bioroebe.calculate_exponential_growth(
+      number_of_cells     = @entry_point_start_with_n_bacteria.text?,
+      number_of_divisions = @entry_point_use_n_divisions.text?
+    )
+    @entry_point_n_cells.set_text(result.to_s)
+  end
+
+  # ========================================================================= #
+  # === create_user_input
+  # ========================================================================= #
+  def create_user_input
+    # ======================================================================= #
+    # === @entry_input_sequence
+    # ======================================================================= #
+    @entry_input_sequence = create_entry
+    @entry_input_sequence.hint =
+      "Input your aminoacid sequence here, then hit the enter-key to "\
+      "evaluate the given input. Invalid entries (aka <b>non-aminoacids</b>) "\
+      "will be filtered away, so do not be surprised if the sequence may "\
+      "be modified (== <b>sanitized</b>).\n\n"\
+      "The cursor-position will indicate at which aminoacid "\
+      "position we are at.\n"
+    @entry_input_sequence.yellow_background
+    @entry_input_sequence.css_class('pad4px')
+    @entry_input_sequence.signal_connect(:event) {|widget, event|
+      if is_mouse_button_release_event?(event)
+        update_information_deduced_from_the_aminoacid_sequence
+      end
+    }
+  end
+
+  # ========================================================================= #
+  # === set_parent_widget
+  # ========================================================================= #
+  def set_parent_widget(i)
+    @parent_widget = i
+  end
+
+  # ========================================================================= #
+  # === fill_the_table_data_with_this_sequence
+  # ========================================================================= #
+  def fill_the_table_data_with_this_sequence(
+      i = @entry_input_sequence.text?
+    )
+    @list_store.clear
+    hash = Bioroebe.return_composition_from_this_aminoacid_sequence(i)
+    array = hash.to_a.map {|inner_array| inner_array.map {|entry| entry.to_s }}
+    ::Gtk.populate_this_liststore(@list_store, array) if use_gtk3?
+  end; alias fill_with_this fill_the_table_data_with_this_sequence # === fill_with_this
+
   # ========================================================================= #
   # === create_then_add_the_header_bar
   # ========================================================================= #
   def create_then_add_the_header_bar
-    require 'bioroebe/gui/gtk3/aminoacid_composition/customized_dialog.rb'
+    require 'bioroebe/gui/universal_widgets/aminoacid_composition/customized_dialog.rb'
     header = return_default_header_bar
     label_description = text(TITLE)
     label_description.make_bold
@@ -239,85 +368,144 @@ EOF
    Compare with this URL:\n
      <a href=\"https://www.selleckchem.com/peptide-calculator.html\" title=\"Another useful resource\">https://www.selleckchem.com/peptide-calculator.html</a>
     "
-    text_widget = gtk_left_aligned_text(content)
+    text_widget = left_aligned_text(content)
     text_widget.use_this_font = :hack_18
     button.on_clicked {
-      ::Bioroebe::GUI::Gtk::CustomizedDialog.new(
-        text_widget
-      )
+      ::Bioroebe::GUI::Gtk::CustomizedDialog.new(text_widget)
     }
     header.pack_start(button)
     minimal(header, 2)
   end
 
   # ========================================================================= #
-  # === update_label_cursor_position
+  # === path_to_the_fasta_file?
   # ========================================================================= #
-  def update_label_cursor_position
-    cursor_position = @entry_input_sequence.cursor_position
-    character = @entry_input_sequence.text?[cursor_position, 1].to_s
-    unless character.empty?
-      _ = 'The aminoacid at position <b>'+
-          (cursor_position+1).to_s+
-          '</b> is: <b>'+character.to_s+'</b>.'
-      @label_cursor_position.set_text(_)
-      @label_cursor_position.do_markify
-    end
+  def path_to_the_fasta_file?
+    ::Bioroebe.log_dir?+
+    'fasta/aminoacid_sequence.fasta'
   end
 
   # ========================================================================= #
-  # === Bioroebe::GUI::Gtk::AminoacidComposition.run
+  # === create_the_skeleton                        (create tag, skeleton tag)
   # ========================================================================= #
-  def self.run(
-      i = ARGV
-    )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::AminoacidComposition.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic
-    r.top_left_then_run
+  def create_the_skeleton
+    create_user_input
+    create_the_treeviews
   end
 
   # ========================================================================= #
-  # === path_to_the_fasta_file?
+  # === create_the_treeviews
   # ========================================================================= #
-  def path_to_the_fasta_file?
-    ::Bioroebe.log_dir?+
-    'fasta/aminoacid_sequence.fasta'
+  def create_the_treeviews
+    # ======================================================================= #
+    # === @list_store
+    # ======================================================================= #
+    @list_store = create_liststore(String, String)
+    # ======================================================================= #
+    # Sort the number of aminoacids a bit differently.
+    # ======================================================================= #
+    @list_store.set_sort_func(1) { |_model, iter1, iter2|
+      iter2[1].to_i <=> iter1[1].to_i
+    }
+    create_the_single_treeview
+    columns = @treeview.columns?
+    columns[0].allow_resizing
+    columns[1].allow_resizing
+    columns[0].sortable_based_on(0)
+    columns[1].sortable_based_on(1)
   end
 
   # ========================================================================= #
-  # === do_open_a_local_FASTA_file
+  # === create_the_buttons                                      (buttons tag)
   # ========================================================================= #
-  def do_open_a_local_FASTA_file(
-      this_widget = @parent_widget
-    )
-    require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
+  def create_the_buttons
+    create_the_button_to_calculate_how_many_bacteria_will_exist
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
+  end
+
+  # ========================================================================= #
+  # === create_the_button_to_calculate_how_many_bacteria_will_exist (button tag)
+  # ========================================================================= #
+  def create_the_button_to_calculate_how_many_bacteria_will_exist
     # ======================================================================= #
-    # We will actively filter for .mp3 files only.
+    # === @button_to_calculate_how_many_bacteria_will_exist
     # ======================================================================= #
-    widget = ::Gtk::SelectFile.new(this_widget) {{
-      filter_for_these_file_types: '.fasta',
-      current_folder:              ::Bioroebe.log_dir?+'fasta/'
-    }}
-    this_file = widget.do_pick_file.text.to_s
-    if File.exist?(this_file) and File.file?(this_file) # Ensure that it really is a file.
-      require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
-      dataset = File.read(this_file)
-      _ = Bioroebe::ParseFasta.new
-      unless dataset.start_with?('--')
-        _.set_data(dataset) # This will use the default file.
-        _.split_into_proper_sections
-        set_main_entry(_.body?)
-        fill_with_this(_.body?)
-        do_update_the_widget_on_the_right_side
+    @button_to_calculate_how_many_bacteria_will_exist = bold_button(
+      '_Calculate how many bacteria will exist after n rounds',
+      self,
+      :use_mnemonic
+    ) {
+      :do_the_calculation
+    }
+    @button_to_calculate_how_many_bacteria_will_exist.clear_background
+    @button_to_calculate_how_many_bacteria_will_exist.bblack2
+    @button_to_calculate_how_many_bacteria_will_exist.hint =
+      "Click on this button in order to do the calculation\n"\
+      "e. g. <b>how many bacteria we will have</b> "\
+      "based on the above parameters."
+    @button_to_calculate_how_many_bacteria_will_exist.on_hover(:powderblue)
+  end
+
+  # ========================================================================= #
+  # === create_the_single_treeview
+  # ========================================================================= #
+  def create_the_single_treeview
+    @treeview = create_tree_view(@list_store) { :clickable_headers }
+    @treeview.set_name('custom_treeview')
+    @treeview.headers('Aminoacid','n times')
+    @treeview.clickable_headers
+    @treeview.set_enable_search(true)
+    @treeview.set_reorderable(true)
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      i = commandline_arguments?
+    )
+    if i.is_a? Array
+      i.each {|entry| menu(entry) }
+    else
+      case i
+      # ===================================================================== #
+      # === gtk_aminoacid_composition --ubi
+      # ===================================================================== #
+      when /^-?-?ubiquitin$/i,
+           /^-?-?ubi$/i
+        set_main_entry(
+          Bioroebe.return_ubiquitin_sequence
+        )
+        simulate_enter_click
       end
     end
-    return this_file
   end
 
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.rb'
+  # ========================================================================= #
+  # === return_widget_containing_the_toolbox_images
+  # ========================================================================= #
+  def return_widget_containing_the_toolbox_images
+    hbox = create_hbox
+    @event_box1 = create_event_box(
+      image_folder_visiting_symbolic
+    )
+    @event_box1.hint =
+      "Click on this image to create a new local "\
+      ".fasta file with that sequence.\n\nThe location will be "\
+      "at: <b>#{path_to_the_fasta_file?}</b>"
+    @event_box1.on_clicked {
+      do_create_a_new_fasta_file
+    }
+    hbox.minimal(@event_box1, 4)
+    return hbox
+  end
+
   # ========================================================================= #
   # === do_create_a_new_fasta_file
   # ========================================================================= #
@@ -374,40 +562,158 @@ EOF
        alias do_update_the_widget_on_the_right_side                 simulate_enter_click # === do_update_the_widget_on_the_right_side
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === create_the_entries                           (entry tag, entries tag)
   # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    create_then_add_the_header_bar
-    if first? and !first?.start_with?('--')
-      @entry_input_sequence.set_text(first?.to_s)
-    end
+  def create_the_entries
     # ======================================================================= #
-    # === @list_store
+    # === @entry_point_start_with_n_bacteria
     # ======================================================================= #
-    @list_store = gtk_liststore(String, String)
+    @entry_point_start_with_n_bacteria = create_entry
+    @entry_point_start_with_n_bacteria.default = 10
+    @entry_point_start_with_n_bacteria.bblack1
+    @entry_point_start_with_n_bacteria.on_click_select_all
+    @entry_point_start_with_n_bacteria.do_center
+    @entry_point_start_with_n_bacteria.on_key_press_event { |widget, event|
+      if use_gtk3?
+        do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
+      else
+        do_the_calculation
+      end
+    }
+    @entry_point_start_with_n_bacteria.hint =
+      'Input a <b>number</b> here, denoting how many bacteria '\
+      'exist at the start.'
+
     # ======================================================================= #
-    # Sort the number of aminoacids a bit differently.
+    # === @entry_point_use_n_divisions
     # ======================================================================= #
-    @list_store.set_sort_func(1) { |_model, iter1, iter2|
-      iter2[1].to_i <=> iter1[1].to_i
+    @entry_point_use_n_divisions = create_entry
+    @entry_point_use_n_divisions.default = 10
+    @entry_point_use_n_divisions.bblack1
+    @entry_point_use_n_divisions.on_click_select_all
+    @entry_point_use_n_divisions.do_center
+    @entry_point_use_n_divisions.on_key_press_event { |widget, event|
+      if use_gtk3?
+        do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
+      else
+        do_the_calculation
+      end
     }
-    create_the_treeview
-    columns = @treeview.columns?
-    columns[0].allow_resizing
-    columns[1].allow_resizing
-    columns[0].sortable_based_on(0)
-    columns[1].sortable_based_on(1)
-    hbox = gtk_hbox
+    @entry_point_use_n_divisions.hint =
+      'Input a <b>number</b> here, denoting how many cell '\
+      'divisions the bacteria will undergo.'
+
+    # ======================================================================= #
+    # === @entry_point_n_cells
+    # ======================================================================= #
+    @entry_point_n_cells = create_entry
+    @entry_point_n_cells.default = 0
+    @entry_point_n_cells.bblack1
+    @entry_point_n_cells.do_center
+    @entry_point_n_cells.on_key_press_event { |widget, event|
+      if use_gtk3?
+        do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
+      else
+        do_the_calculation
+      end
+    }
+    @entry_point_n_cells.hint =
+      'The number here will be <b>the amount of bacteria '\
+      'after n cell divisions</b>.'
+  end
+
+  # ========================================================================= #
+  # === create_the_boxes
+  # ========================================================================= #
+  def create_the_boxes
+    # ======================================================================= #
+    # === @hbox1
+    # ======================================================================= #
+    @hbox1 = create_hbox(
+      bold_text('n bacteria (start)'),
+      @entry_point_start_with_n_bacteria
+    )
+
+    # ======================================================================= #
+    # === @hbox2
+    # ======================================================================= #
+    @hbox2 = create_hbox(
+      bold_text('n doubling times'),
+      @entry_point_use_n_divisions
+    )
+
+    # ======================================================================= #
+    # === @hbox3
+    # ======================================================================= #
+    @hbox3 = create_hbox(
+      bold_text('n bacteria (end)'),
+      @entry_point_n_cells
+    )
+  end
+
+  # ========================================================================= #
+  # === create_the_hspacer
+  # ========================================================================= #
+  def create_the_hspacer
+    @a_hspacer = create_hspacer
+  end
+
+  # ========================================================================= #
+  # === do_open_a_local_FASTA_file
+  # ========================================================================= #
+  def do_open_a_local_FASTA_file(
+      this_widget = @parent_widget
+    )
+    require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
+    # ======================================================================= #
+    # We will actively filter for .mp3 files only.
+    # ======================================================================= #
+    widget = ::Gtk::SelectFile.new(this_widget) {{
+      filter_for_these_file_types: '.fasta',
+      current_folder:              ::Bioroebe.log_dir?+'fasta/'
+    }}
+    this_file = widget.do_pick_file.text.to_s
+    if File.exist?(this_file) and File.file?(this_file) # Ensure that it really is a file.
+      require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+      dataset = File.read(this_file)
+      _ = Bioroebe::ParseFasta.new
+      unless dataset.start_with?('--')
+        _.set_data(dataset) # This will use the default file.
+        _.split_into_proper_sections
+        set_main_entry(_.body?)
+        fill_with_this(_.body?)
+        do_update_the_widget_on_the_right_side
+      end
+    end
+    return this_file
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+
+    menu
+    vbox = create_vbox
+    
+    create_then_add_the_header_bar if use_gtk3?
+
+    if first? and !first?.start_with?('--')
+      @entry_input_sequence.set_text(first?.to_s)
+    end
+
+    hbox = create_hbox
     hbox.maximal(@entry_input_sequence, 6)
-    event_box = gtk_event_box(image_file_open)
+    event_box = create_event_box(image_file_open)
     event_box.hint = 'Click on this button in order to '\
       'open a local .FASTA file.'
     event_box.on_clicked {
-      do_open_a_local_FASTA_file
+      do_open_a_local_FASTA_file if use_gtk3?
     }
     hbox.minimal(event_box,       1)
-    add(hbox)
+
+    vbox.minimal(hbox, 1)
     @entry_input_sequence.on_enter {
       simulate_enter_click
     }
@@ -427,50 +733,44 @@ EOF
     small_vbox.minimal(return_widget_containing_the_toolbox_images, 5)
     _ = draggable_from_left_to_right(scrolled_window, small_vbox)
     _.position = 350
-    minimal(_, 1)
+    
+    vbox.minimal(_, 1)
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << vbox
+    ::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.top_left
+    run_main
   end
 
   # ========================================================================= #
-  # === create_the_treeview
+  # === Bioroebe::GUI::UniversalWidgets::AminoacidComposition[]
   # ========================================================================= #
-  def create_the_treeview
-    @treeview = create_tree_view(@list_store) { :clickable_headers }
-    @treeview.set_name('custom_treeview')
-    @treeview.headers('Aminoacid','n times')
-    @treeview.clickable_headers
-    @treeview.set_enable_search(true)
-    @treeview.set_reorderable(true)
+  def self.[](i = ARGV)
+    new(i)
   end
 
   # ========================================================================= #
-  # === return_widget_containing_the_toolbox_images
+  # === Bioroebe::GUI::Gtk::AminoacidComposition.run
   # ========================================================================= #
-  def return_widget_containing_the_toolbox_images
-    hbox = create_hbox
-    @event_box1 = create_event_box(
-      image_folder_visiting_symbolic
+  def self.run(
+      i = ARGV
     )
-    @event_box1.hint =
-      "Click on this image to create a new local "\
-      ".fasta file with that sequence.\n\nThe location will be "\
-      "at: <b>#{path_to_the_fasta_file?}</b>"
-    @event_box1.on_clicked {
-      do_create_a_new_fasta_file
-    }
-    hbox.minimal(@event_box1, 4)
-    return hbox
-  end
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    super()
-    menu
-  end
+    ::Gtk.gtk_runner_factory(
+      ::Bioroebe::GUI::Gtk::AminoacidComposition.new(i)
+    )
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::AminoacidComposition.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::AminoacidComposition.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::AminoacidComposition.run
+  Bioroebe::GUI::UniversalWidgets::AminoacidComposition.new(ARGV)
 end # gtkaa --ubi