bioroebe 0.12.24 → 0.13.31

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

@@ -2,60 +2,102 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::NucleotideAnalyser
+# === Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
-# Bioroebe::GUI::Gtk::NucleotideAnalyser.run
+# require 'bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb'
 # =========================================================================== #
-require 'gtk_paradise/require_gtk3'
+require 'universal_widgets/base/base.rb'
 
 module Bioroebe
 
 module GUI
 
-module Gtk
+module UniversalWidgets
 
-class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalyser 
+class NucleotideAnalyser < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser
 
-  require 'bioroebe/calculate/calculate_gc_content.rb'
-  require 'gtk_paradise/widgets/gtk3/select_file/select_file.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
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/calculate/calculate_gc_content.rb'
+  require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
 
   # ========================================================================= #
   # === TITLE
+  #
+  # Specify which title to use for this widget.
   # ========================================================================= #
   TITLE = 'Nucleotide Analyser'
 
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH = '65% or minimum 350px'
+  WIDTH = '75% or 1200px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = 580
+  HEIGHT = '55% or 500px minimum'
+
+  # ========================================================================= #
+  # === FONT_LARGE
+  # ========================================================================= #
+  FONT_LARGE = 'Calibri 32'
+
+  # ========================================================================= #
+  # === MONOSPACED_FONT
+  #
+  # When this font is changed, don't forget to also change the font
+  # at SMALLER_FONT.
+  # ========================================================================= #
+  MONOSPACED_FONT = :hack_22
+    USE_THIS_FONT = MONOSPACED_FONT
+    USE_THIS_MONOFONT = MONOSPACED_FONT
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
 
   # ========================================================================= #
-  # === USE_THIS_FONT
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
   # ========================================================================= #
-  USE_THIS_FONT = :hack_16
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_HEADER
+  # ========================================================================= #
+  USE_THIS_HEADER = ['one-letter abbreviation', 'n times']
+
+  # ========================================================================= #
+  # === GENERATE_N_AMINOACIDS_BY_DEFAULT
+  # ========================================================================= #
+  GENERATE_N_AMINOACIDS_BY_DEFAULT = 15
+
+  # ========================================================================= #
+  # === COLOUR_FOR_NON_MATCHES
+  #
+  # This is the colour that will be used for non-matching nucleotides.
+  # ========================================================================= #
+  COLOUR_FOR_NON_MATCHES = :magenta
 
   # ========================================================================= #
   # === 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
@@ -67,14 +109,19 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   # === 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(10)
+    handle_CSS if use_gtk3?
     # ======================================================================= #
     # === @sequence
     # ======================================================================= #
@@ -82,54 +129,69 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
                 'ATGCTAGTCAGTCAGTCGATGTGCATGCTAGTCAGTCAGTCGATGCA'
     # ^^^ overrule for now.
     initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
-    handle_CSS_rules
   end
 
   # ========================================================================= #
-  # === initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
+  # === create_the_entries                                        (entry tag)
   # ========================================================================= #
-  def initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets(
-      i = @sequence
-    )
+  def create_the_entries
     # ======================================================================= #
-    # Specify the dataset that we wish to use for the gtk_table3() call.
+    # === @entry_input_sequence
     # ======================================================================= #
-    @dataset = return_dataset_based_on_this_sequence(i)
-    @tree_view, @list_store = gtk_table3(
-      @dataset
-    ) {{
-      cell_renderer_text1: :align_to_the_middle,
-      cell_renderer_text2: :align_to_the_middle
-    }}
-    @tree_view.bblack2
-    @tree_view.pad10px
-    @tree_view.set_name('custom_treeview')
-    @tree_view.first_column?.center
-    @tree_view.second_column?.center
-    @tree_view.the_headers_can_be_moved
+    @entry_input_sequence = entry
+    @entry_input_sequence.default_values
+    @entry_input_sequence.hint = 'The sequence will be evaluated '\
+      'whenever it is changed, as-is. Hit the <b>enter</b> key '\
+      'to change it, for convenience.'
+    @entry_input_sequence.on_changed {
+      update_the_main_sequence_variable
+      update_this_sequence_contains_n_nucleotides
+      update_the_table_dataset
+      update_the_labels
+    }
+    # ======================================================================= #
+    # Act on when the user hits the enter-key.
+    # ======================================================================= #
+    @entry_input_sequence.on_enter_key {
+      sanitize_the_sequence
+      do_analyse_the_sequence
+      update_this_sequence_contains_n_nucleotides(
+        return_how_many_nucleotides_this_sequence_contains
+      )
+    }
   end
 
   # ========================================================================= #
-  # === padding?
+  # === entry_input_sequence?
   # ========================================================================= #
-  def padding?
-    2
+  def entry_input_sequence?
+    @entry_input_sequence
+  end; alias main_entry? entry_input_sequence? # === main_entry?
+
+  # ========================================================================= #
+  # === dna_sequence?
+  # ========================================================================= #
+  def dna_sequence?
+    @entry_input_sequence.text?
   end
 
   # ========================================================================= #
-  # === border_size?
+  # === update_the_GC_content_label
   # ========================================================================= #
-  def border_size?
-    2
+  def update_the_GC_content_label
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_GC_content.set_text(
+      'The <b>GC content</b> (G+C) is: <b>'+_.to_s+'%</b>'
+    )
+    @label_GC_content.do_markify
   end
 
   # ========================================================================= #
-  # === create_skeleton                                          (create tag)
+  # === update_the_labels
   # ========================================================================= #
-  def create_skeleton
-    create_buttons
-    create_the_labels
-    create_entry
+  def update_the_labels
+    update_the_GC_content_label
+    update_the_AT_content_label
   end
 
   # ========================================================================= #
@@ -196,42 +258,6 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
     end
   end
 
-  # ========================================================================= #
-  # === create_buttons                              (buttons tag, button tag)
-  # ========================================================================= #
-  def create_buttons
-    # ======================================================================= #
-    # === @button_reset
-    # ======================================================================= #
-    @button_reset = button('_Reset the table')
-    @button_reset.hint = 'This button will clear the table-result '\
-                         'shown above.'
-    @button_reset.on_clicked {
-      clear_table
-    }
-    # ======================================================================= #
-    # === @button_reset_the_input_sequence
-    # ======================================================================= #
-    @button_reset_the_input_sequence = button('Reset the _input sequence')
-    @button_reset_the_input_sequence.enable_markup
-    @button_reset_the_input_sequence.hint = 'This button will '\
-      'reset (aka clear) the input sequence. The input sequence is kept '\
-      'on top of this widget, as a gtk-entry.'
-    @button_reset_the_input_sequence.on_clicked {
-      do_reset_the_input_sequence
-    }
-    # ======================================================================= #
-    # === @button_open_file
-    # ======================================================================= #
-    @button_open_file = button('_Open file')
-    @button_open_file.enable_markup
-    @button_open_file.hint = 'This button can be used to open a local'\
-                             'file, typically a FASTA (.fasta) file.'
-    @button_open_file.on_clicked {
-      do_open_a_local_file
-    }
-  end
-
   # ========================================================================= #
   # === update_this_sequence_contains_n_nucleotides
   # ========================================================================= #
@@ -298,47 +324,105 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   end
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === update_the_AT_content_label
   # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    _ = first_argument?.to_s
-    minimal(@entry_input_sequence, 2)
-    @entry_input_sequence.set_text(@sequence.to_s)
-    minimal(@text_this_sequence_contains, 2)
-    minimal(gtk_horizontal_spacer)
-    @tree_view.all_are_sortable # Make them all sortable.
-    scrolled_window = gtk_scrolled_window(@tree_view) { :never_always }
-    scrolled_window.set_size_request(420, 260)
-    minimal(scrolled_window, 5)
-    minimal(gtk_horizontal_spacer)
-    update_the_labels
-    minimal(@label_GC_content)
-    minimal(@label_AT_content)
-    hbox = gtk_hbox
-    hbox.maximal(@button_reset,                    1)
-    hbox.maximal(@button_reset_the_input_sequence, 1)
-    hbox.maximal(@button_open_file,                1)
-    minimal(hbox, 2)
+  def update_the_AT_content_label
+    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
+    @label_AT_content.set_text(
+      "The <b>AT content</b> (A+T) is: <b>"\
+      "#{(100.0 - _.to_f).round(1).to_s}%</b>"
+    )
+    @label_AT_content.do_markify
   end
 
   # ========================================================================= #
-  # === handle_CSS_rules                                            (CSS tag)
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_input_sequence.set_text(i.to_s)
+  end; alias set_dna_sequence set_main_entry # === set_dna_sequence
+
+  # ========================================================================= #
+  # === create_the_buttons                          (buttons tag, button tag)
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @button_reset
+    # ======================================================================= #
+    @button_reset = button('_Reset the table')
+    @button_reset.hint = 'This button will clear the table-result '\
+                         'shown above.'
+    @button_reset.on_clicked {
+      clear_table
+    }
+    # ======================================================================= #
+    # === @button_reset_the_input_sequence
+    # ======================================================================= #
+    @button_reset_the_input_sequence = button('Reset the _input sequence')
+    @button_reset_the_input_sequence.enable_markup
+    @button_reset_the_input_sequence.hint = 'This button will '\
+      'reset (aka clear) the input sequence. The input sequence is kept '\
+      'on top of this widget, as a gtk-entry.'
+    @button_reset_the_input_sequence.on_clicked {
+      do_reset_the_input_sequence
+    }
+    # ======================================================================= #
+    # === @button_open_file
+    # ======================================================================= #
+    @button_open_file = button('_Open file')
+    @button_open_file.enable_markup
+    @button_open_file.hint = 'This button can be used to open a local'\
+                             'file, typically a FASTA (.fasta) file.'
+    @button_open_file.on_clicked {
+      do_open_a_local_file
+    }
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    2
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  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
-    append_these_custom_CSS_rules '
+    append_project_css_file
+    add_these_custom_CSS_rules '
+
 #custom_treeview.view header button {
   color: royalblue;
   font-weight: bold;
   font-size: larger;
   padding: 8px;
 }
-
 '
     apply_the_CSS_rules
-  end
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
 
   # ========================================================================= #
   # === create_the_labels
@@ -366,93 +450,100 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   end
 
   # ========================================================================= #
-  # === create_entry                                              (entry tag)
-  # ========================================================================= #
-  def create_entry
-    # ======================================================================= #
-    # === @entry_input_sequence
-    # ======================================================================= #
-    @entry_input_sequence = entry
-    @entry_input_sequence.default_values
-    @entry_input_sequence.hint = 'The sequence will be evaluated '\
-      'whenever it is changed, as-is. Hit the <b>enter</b> key '\
-      'to change it, for convenience.'
-    @entry_input_sequence.on_changed {
-      update_the_main_sequence_variable
-      update_this_sequence_contains_n_nucleotides
-      update_the_table_dataset
-      update_the_labels
-    }
-    # ======================================================================= #
-    # Act on when the user hits the enter-key.
-    # ======================================================================= #
-    @entry_input_sequence.on_enter_key {
-      sanitize_the_sequence
-      do_analyse_the_sequence
-      update_this_sequence_contains_n_nucleotides(
-        return_how_many_nucleotides_this_sequence_contains
-      )
-    }
-  end
-
-  # ========================================================================= #
-  # === entry_input_sequence?
-  # ========================================================================= #
-  def entry_input_sequence?
-    @entry_input_sequence
-  end; alias main_entry? entry_input_sequence? # === main_entry?
-
-  # ========================================================================= #
-  # === dna_sequence?
+  # === create_the_skeleton                        (create tag, skeleton tag)
   # ========================================================================= #
-  def dna_sequence?
-    @entry_input_sequence.text?
+  def create_the_skeleton
+    create_the_labels
+    create_the_entries
+    create_the_buttons
   end
 
   # ========================================================================= #
-  # === update_the_GC_content_label
+  # === run                                                         (run tag)
   # ========================================================================= #
-  def update_the_GC_content_label
-    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
-    @label_GC_content.set_text(
-      'The <b>GC content</b> (G+C) is: <b>'+_.to_s+'%</b>'
-    )
-    @label_GC_content.do_markify
+  def run
+    run_super
   end
 
   # ========================================================================= #
-  # === update_the_labels
+  # === smaller_font?
   # ========================================================================= #
-  def update_the_labels
-    update_the_GC_content_label
-    update_the_AT_content_label
+  def smaller_font?
+    SMALLER_FONT
   end
 
   # ========================================================================= #
-  # === update_the_AT_content_label
+  # === initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
   # ========================================================================= #
-  def update_the_AT_content_label
-    _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
-    @label_AT_content.set_text(
-      "The <b>AT content</b> (A+T) is: <b>"\
-      "#{(100.0 - _.to_f).round(1).to_s}%</b>"
+  def initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets(
+      i = @sequence
     )
-    @label_AT_content.do_markify
+    # ======================================================================= #
+    # Specify the dataset that we wish to use for the gtk_table3() call.
+    # ======================================================================= #
+    @dataset = return_dataset_based_on_this_sequence(i)
+    @tree_view, @list_store = gtk_table3(
+      @dataset
+    ) {{
+      cell_renderer_text1: :align_to_the_middle,
+      cell_renderer_text2: :align_to_the_middle
+    }}
+    @tree_view.bblack2
+    @tree_view.pad10px
+    @tree_view.set_name('custom_treeview')
+    @tree_view.first_column?.center
+    @tree_view.second_column?.center
+    @tree_view.the_headers_can_be_moved
   end
 
   # ========================================================================= #
-  # === set_main_entry
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
   # ========================================================================= #
-  def set_main_entry(i)
-    @entry_input_sequence.set_text(i.to_s)
-  end; alias set_dna_sequence set_main_entry # === set_dna_sequence
+  def connect_the_skeleton
+    abort_on_exception
+    
+    @outer_vbox = create_vbox
+    
+    _ = first_argument?.to_s
+    @outer_vbox.minimal(@entry_input_sequence, 2)
+    @entry_input_sequence.set_text(@sequence.to_s)
+    @outer_vbox.minimal(@text_this_sequence_contains, 2)
+    @outer_vbox.minimal(horizontal_spacer)
+    @tree_view.all_are_sortable # Make them all sortable.
+    scrolled_window = create_scrolled_window(@tree_view) { :never_always }
+    scrolled_window.set_size_request(420, 260)
+    @outer_vbox.minimal(scrolled_window, 5)
+    @outer_vbox.minimal(gtk_horizontal_spacer)
+    update_the_labels
+    @outer_vbox.minimal(@label_GC_content)
+    @outer_vbox.minimal(@label_AT_content)
+    hbox = create_hbox
+    hbox.maximal(@button_reset,                    1)
+    hbox.maximal(@button_reset_the_input_sequence, 1)
+    hbox.maximal(@button_open_file,                1)
+    @outer_vbox.minimal(hbox, 2)
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << @outer_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?)
+    do_style_all_buttons_in_a_uniform_manner
+    window.top_left
+    run_main
+  end
 
   # ========================================================================= #
-  # === run                                                         (run tag)
+  # === Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser[]
   # ========================================================================= #
-  def run
-    create_skeleton_then_connect_skeleton
-    do_style_all_buttons_in_a_uniform_manner
+  def self.[](i = ARGV)
+    new(i)
   end
 
   # ========================================================================= #
@@ -461,15 +552,16 @@ class NucleotideAnalyser < ::Gtk::Box # === Bioroebe::GUI::Gtk::NucleotideAnalys
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::NucleotideAnalyser.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_top_left_then_run
-  end
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::NucleotideAnalyser.new(i)
+    )
+    r.background_colour(:white)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::NucleotideAnalyser.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::NucleotideAnalyser.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::NucleotideAnalyser.run
-end
+  Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser.new(ARGV)
+end # gtkNucleotideAnalyser