bioroebe 0.12.24 → 0.13.31

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

@@ -2,76 +2,90 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::RestrictionEnzymes
+# === Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes
 #
 # The basic idea for this widget is to tie functionality related to
 # choosing restriction enzymes into one widget.
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb'
-# Bioroebe::GUI::Gtk::RestrictionEnzymes.run
+# require 'bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb'
 # =========================================================================== #
-require 'gtk_paradise/require_gtk3'
+require 'universal_widgets/base/base.rb'
 
 module Bioroebe
 
 module GUI
 
-module Gtk
+module UniversalWidgets
 
-class RestrictionEnzymes < ::Gtk::Box # === Bioroebe::GUI::Gtk::RestrictionEnzymes 
+class RestrictionEnzymes < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes
 
-  require 'bioroebe/enzymes/restriction_enzymes_file.rb'
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
 
   require 'bioroebe/constants/GUIs.rb'
-  include ::Bioroebe::GUI::Gtk
   include Bioroebe::GUI
 
-  require 'gtk_paradise/requires/require_the_base_module.rb'
-  include ::Gtk::BaseModule
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/enzymes/restriction_enzymes_file.rb'
 
   # ========================================================================= #
-  # === NAMESPACE
+  # === TITLE
+  #
+  # Specify which title to use for this small widget.
   # ========================================================================= #
-  NAMESPACE = inspect
+  TITLE = 'Restriction Enzymes'
 
   # ========================================================================= #
-  # === TITLE
+  # === WIDTH
   # ========================================================================= #
-  TITLE = 'Restriction Enzymes'
+  WIDTH = '65% or 600px minimum'
 
   # ========================================================================= #
-  # === FILE_RESTRICTION_ENZYMES
+  # === HEIGHT
   # ========================================================================= #
-  FILE_RESTRICTION_ENZYMES = ::Bioroebe.restriction_enzymes_file?
+  HEIGHT = '55% or 400px minimum'
 
   # ========================================================================= #
-  # === WIDTH
+  # === MONOSPACED_FONT
+  #
+  # When this font is changed, don't forget to also change the font
+  # at SMALLER_FONT.
   # ========================================================================= #
-  WIDTH = 940
+  MONOSPACED_FONT = :hack_20
+    USE_THIS_FONT = MONOSPACED_FONT
 
   # ========================================================================= #
-  # === HEIGHT
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
+
   # ========================================================================= #
-  HEIGHT = '20% or minimum 200px'
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
 
   # ========================================================================= #
-  # === USE_THIS_FONT
+  # === FILE_RESTRICTION_ENZYMES
   # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_21
+  FILE_RESTRICTION_ENZYMES = ::Bioroebe.restriction_enzymes_file?
 
   # ========================================================================= #
   # === 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
     )
-    modify_background(:normal, :white)
     run if run_already
   end
 
@@ -79,15 +93,19 @@ class RestrictionEnzymes < ::Gtk::Box # === Bioroebe::GUI::Gtk::RestrictionEnzym
   # === 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)
-    use_gtk_paradise_project_css_file
-    append_project_css_file 
-    infer_the_size_automatically
+    handle_CSS if use_gtk3?
     # ======================================================================= #
     # === @hash_restriction_enzymes
     # ======================================================================= #
@@ -107,74 +125,101 @@ class RestrictionEnzymes < ::Gtk::Box # === Bioroebe::GUI::Gtk::RestrictionEnzym
   # === padding?
   # ========================================================================= #
   def padding?
-    6
+    8
   end
 
   # ========================================================================= #
   # === border_size?
   # ========================================================================= #
   def border_size?
-    0
+    2
   end
 
   # ========================================================================= #
-  # === load_yaml_file
+  # === main_font?
   # ========================================================================= #
-  def load_yaml_file(
-      i = FILE_RESTRICTION_ENZYMES
-    )
-    @yaml = YAML.load_file(i)
+  def main_font?
+    USE_THIS_FONT
   end
 
   # ========================================================================= #
-  # === create_combo_box
-  #
-  # rf gtk combobox
+  # === slightly_smaller_font?
   # ========================================================================= #
-  def create_combo_box
-    @combo_box = gtk_combo_box(:strings_only)
-    @combo_box.bblack1
-    @combo_box.use_this_font(:hack_21)
-    @yaml.each {|name_of_the_restriction_enzyme, cuts_at_this_location|
-      # ===================================================================== #
-      # The entries will be like this:
-      #   ["PshBI", "ATTAAT   2"]
-      # ===================================================================== #
-      @hash_restriction_enzymes[name_of_the_restriction_enzyme] =
-        cuts_at_this_location
-      _ = "#{name_of_the_restriction_enzyme.ljust(10,' ')} → #{cuts_at_this_location}"
-      @combo_box.append_text(_)
-    }
-    @combo_box.on_changed {
-      if @combo_box.active_iter
-        _ = @combo_box.active_iter[0]
-        @entry_selection.set_text(_)
-        if _.include? '→'
-          _ = _.split('→').last.strip.split(' ').first.to_s
-        end
-        @entry_showing_only_the_sequence_that_is_to_be_cut.set_text(_)
-      end
+  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 '
+
+    '
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === create_the_entries                           (entries tag, entry tag)
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # === @entry_showing_only_the_sequence_that_is_to_be_cut
+    # ======================================================================= #
+    @entry_showing_only_the_sequence_that_is_to_be_cut = create_entry
+    @entry_showing_only_the_sequence_that_is_to_be_cut.width_height(400, 42)
+    @entry_showing_only_the_sequence_that_is_to_be_cut.clear_background
+    @entry_showing_only_the_sequence_that_is_to_be_cut.make_bold
+    @entry_showing_only_the_sequence_that_is_to_be_cut.align_to_the_center
+    @entry_showing_only_the_sequence_that_is_to_be_cut.bblack2
+    @entry_showing_only_the_sequence_that_is_to_be_cut.very_light_yellowish_background
+    @entry_showing_only_the_sequence_that_is_to_be_cut.hint = 
+      'This entry shows at which sequence the selected restriction '\
+      'enzyme will cut.'
+    # ======================================================================= #
+    # === @entry_selection
+    # ======================================================================= #
+    @entry_selection = create_entry
+    @entry_selection.clear_background
+    @entry_selection.bblack1
+    @entry_selection.width_height(540, 42)
+    @entry_selection.on_button_press_event { |widget, event|
+      @entry_selection.set_focus(true)
+      # @entry_selection.select_everything
     }
-    @combo_box.active = 0
   end
 
   # ========================================================================= #
-  # === add_status_message
+  # === create_status_bar
   # ========================================================================= #
-  def add_status_message(i)
-    @statusbar.set_text(i)
-    @statusbar.do_markify
+  def create_status_bar
+    # ======================================================================= #
+    # === @statusbar
+    # ======================================================================= #
+    @statusbar = create_label
+    @statusbar.align_left
+  end
+
+  # ========================================================================= #
+  # === load_yaml_file
+  # ========================================================================= #
+  def load_yaml_file(
+      i = FILE_RESTRICTION_ENZYMES
+    )
+    @yaml = YAML.load_file(i)
   end
 
   # ========================================================================= #
   # === return_widget_in_the_second_row_starting_with_a_gtk_entry_widget
   # ========================================================================= #
   def return_widget_in_the_second_row_starting_with_a_gtk_entry_widget
-    hbox = gtk_hbox
+    hbox = create_hbox
     # ======================================================================= #
     # === @entry_search
     # ======================================================================= #
-    @entry_search = gtk_search_entry
+    @entry_search = create_search_entry
     @entry_search.clear_background
     @entry_search.bblack1
     @entry_search.on_enter {
@@ -221,64 +266,109 @@ class RestrictionEnzymes < ::Gtk::Box # === Bioroebe::GUI::Gtk::RestrictionEnzym
   end
 
   # ========================================================================= #
-  # === create_skeleton                                          (create tag)
+  # === create_the_combo_box
+  #
+  # rf gtk combobox
   # ========================================================================= #
-  def create_skeleton
-    create_entries
-    create_combo_box
-    create_status_bar
+  def create_the_combo_box
+    @combo_box = create_combo_box(:strings_only)
+    @combo_box.bblack1
+    @combo_box.use_this_font(:hack_21)
+    @yaml.each {|name_of_the_restriction_enzyme, cuts_at_this_location|
+      # ===================================================================== #
+      # The entries will be like this:
+      #   ["PshBI", "ATTAAT   2"]
+      # ===================================================================== #
+      @hash_restriction_enzymes[name_of_the_restriction_enzyme] =
+        cuts_at_this_location
+      _ = "#{name_of_the_restriction_enzyme.ljust(10,' ')} → #{cuts_at_this_location}"
+      @combo_box.append_text(_)
+    }
+    @combo_box.on_changed {
+      if @combo_box.active_iter
+        _ = @combo_box.active_iter[0]
+        @entry_selection.set_text(_)
+        if _.include? '→'
+          _ = _.split('→').last.strip.split(' ').first.to_s
+        end
+        @entry_showing_only_the_sequence_that_is_to_be_cut.set_text(_)
+      end
+    }
+    @combo_box.active = 0
   end
 
   # ========================================================================= #
-  # === create_status_bar
+  # === add_status_message
   # ========================================================================= #
-  def create_status_bar
-    # ======================================================================= #
-    # === @statusbar
-    # ======================================================================= #
-    @statusbar = gtk_label
-    @statusbar.align_left
+  def add_status_message(i)
+    @statusbar.set_text(i)
+    @statusbar.do_markify
+    return @statusbar
   end
 
   # ========================================================================= #
-  # === create_entries                               (entries tag, entry tag)
+  # === create_the_skeleton                        (create tag, skeleton tag)
   # ========================================================================= #
-  def create_entries
-    # ======================================================================= #
-    # === @entry_showing_only_the_sequence_that_is_to_be_cut
-    # ======================================================================= #
-    @entry_showing_only_the_sequence_that_is_to_be_cut = gtk_entry
-    @entry_showing_only_the_sequence_that_is_to_be_cut.width_height(400, 42)
-    @entry_showing_only_the_sequence_that_is_to_be_cut.clear_background
-    @entry_showing_only_the_sequence_that_is_to_be_cut.make_bold
-    @entry_showing_only_the_sequence_that_is_to_be_cut.align_to_the_center
-    @entry_showing_only_the_sequence_that_is_to_be_cut.bblack2
-    @entry_showing_only_the_sequence_that_is_to_be_cut.very_light_yellowish_background
-    @entry_showing_only_the_sequence_that_is_to_be_cut.hint = 
-      'This entry shows at which sequence the selected restriction '\
-      'enzyme will cut.'
-    # ======================================================================= #
-    # === @entry_selection
-    # ======================================================================= #
-    @entry_selection = gtk_entry
-    @entry_selection.clear_background
-    @entry_selection.bblack1
-    @entry_selection.width_height(540, 42)
-    @entry_selection.on_button_press_event { |widget, event|
-      @entry_selection.set_focus(true)
-      # @entry_selection.select_everything
-    }
+  def create_the_skeleton
+    create_the_entries
+    create_the_combo_box
+    create_status_bar
   end
 
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
-    super()
+    run_super
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+
+    vbox = create_vbox
+    
+    text1 = selectable_text('<b>'+@yaml.keys.size.to_s+'</b> restriction enzymes '\
+            'are registered.')
+    vbox.minimal(text1, 1)
+    hbox1 = create_hbox
+    hbox1.minimal(@combo_box,       5)
+    hbox1.minimal(@entry_selection, 5)
+    vbox.minimal(hbox1, 1)
+    vbox.minimal(return_widget_in_the_second_row_starting_with_a_gtk_entry_widget, 1)
+    vbox.minimal(@statusbar, 1)
+    # ======================================================================= #
+    # Show a simple status-message on the bottom of this widget.
+    # ======================================================================= #
+    add_status_message('')
+
+    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
     Thread.new {
       sleep 0.0001
       @entry_search.do_focus
     }
+    run_main
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
   end
 
   # ========================================================================= #
@@ -287,42 +377,22 @@ class RestrictionEnzymes < ::Gtk::Box # === Bioroebe::GUI::Gtk::RestrictionEnzym
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::RestrictionEnzymes.new(i)
-    r = ::Gtk.run
-    r << _
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::RestrictionEnzymes.new(i)
+    )
+    r.modify_background(:normal, :mintcream)
     r.set_border_width(4)
     r.add_shortcut(1, 'focus_entry(1)', :alt)
     r.add_shortcut(2, 'focus_entry(2)', :alt)
     r.add_shortcut(3, 'focus_entry(3)', :alt)
     r.add_shortcut(4, 'focus_entry(4)', :alt)
     r.background_colour :whitesmoke
-    r.automatic_top_left_then_run
-  end; self.instance_eval { alias start_gui_application run } # === RestrictionEnzymesModule.start_gui_application
-       self.instance_eval { alias run_gtk3_widget       run } # === RestrictionEnzymesModule.run_gtk3_widget
-
-  # ========================================================================= #
-  # === connect_skeleton                                         (skeleton tag)
-  # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    text1 = selectable_text('<b>'+@yaml.keys.size.to_s+'</b> restriction enzymes '\
-            'are registered.')
-    minimal(text1, 1)
-    hbox1 = hbox
-    hbox1.minimal(@combo_box,       5)
-    hbox1.minimal(@entry_selection, 5)
-    minimal(hbox1, 1)
-    minimal(return_widget_in_the_second_row_starting_with_a_gtk_entry_widget, 1)
-    minimal(@statusbar, 1)
-    # ======================================================================= #
-    # Show a simple status-message on the bottom of this widget.
-    # ======================================================================= #
-    add_status_message('')
-  end
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::RestrictionEnzymes.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::RestrictionEnzymes.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::RestrictionEnzymes.run
-end
+  Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes.new(ARGV)
+end # gtkRestrictionEnzymes