bioroebe 0.12.24 → 0.13.31

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

@@ -2,59 +2,89 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::FormatConverter
+# === Bioroebe::GUI::UniversalWidgets::FormatConverter
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::FormatConverter.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/format_converter/format_converter.rb'
-# Bioroebe::GUI::Gtk::FormatConverter.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 FormatConverter < ::Gtk::Box # === Bioroebe::GUI::Gtk::FormatConverter 
+class FormatConverter < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::FormatConverter
 
-  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
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/log_directory/log_directory.rb'
 
   # ========================================================================= #
   # === TITLE
+  #
+  # Specify which title to use for this widget.
   # ========================================================================= #
   TITLE = 'Format Converter'
 
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH = '60% or 800px minimum'
+  WIDTH = '75% or 2000px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = 800
+  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_20
+    USE_THIS_FONT = MONOSPACED_FONT
+    USE_THIS_MONOFONT = MONOSPACED_FONT
 
   # ========================================================================= #
-  # === USE_THIS_FONT
+  # === SMALLER_FONT
   # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_20
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === TEXT1
+  # ========================================================================= #
+  TEXT1 = 'Available BLOSUM matrices:'
 
   # ========================================================================= #
   # === 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
@@ -66,15 +96,19 @@ class FormatConverter < ::Gtk::Box # === Bioroebe::GUI::Gtk::FormatConverter
   # === 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?
   end
 
   # ========================================================================= #
@@ -92,94 +126,48 @@ class FormatConverter < ::Gtk::Box # === Bioroebe::GUI::Gtk::FormatConverter
   end
 
   # ========================================================================= #
-  # === create_user_input
-  # ========================================================================= #
-  def create_user_input
-    # ======================================================================= #
-    # === @entry_input_sequence
-    # ======================================================================= #
-    @entry_input_sequence = gtk_entry
-    @entry_input_sequence.hint = 'This will denote the current file.'
-    @entry_input_sequence.bblack1
-    @entry_input_sequence.yellow_background
-    @entry_input_sequence.pad5px
-  end
-
-  # ========================================================================= #
-  # === set_parent_widget
+  # === main_font?
   # ========================================================================= #
-  def set_parent_widget(i)
-    @parent_widget = i
+  def main_font?
+    USE_THIS_FONT
   end
 
   # ========================================================================= #
-  # === fill_with_this
+  # === slightly_smaller_font?
   # ========================================================================= #
-  def fill_with_this(i)
-    @text_buffer.set_text(i)
+  def slightly_smaller_font?
+    USE_THIS_SLIGHTLY_SMALLER_FONT
   end
 
   # ========================================================================= #
-  # === calculated_weight?
+  # === handle_CSS_rules                                   (CSS tag, css tag)
   # ========================================================================= #
-  def calculated_weight?(i)
-    this_file = Bioroebe.file_molecular_weight
-    dataset = YAML.load_file(this_file)
-    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
-    # ======================================================================= #
-    # Must deduct water too.
-    # ======================================================================= #
-    weight -= (18.0 * (i.size - 1))
-    return weight.round(2)
-  end
+  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
 
   # ========================================================================= #
-  # === simulate_enter_click
+  # === do_open_a_local_file
   # ========================================================================= #
-  def simulate_enter_click(
-      _ = @entry_input_sequence.text?
-    )
-    _.upcase!
-    _ = ::Bioroebe.filter_away_invalid_aminoacids(_)
-    @entry_input_sequence.set_text(_)
-    fill_the_table_data_with_this_sequence(_)
-    @label_n_aminoacids.set_text(
-      "This sequence has <b>#{_.size}</b> aminoacids."
-    )
-    @label_n_aminoacids.do_markify
-    @label_molecular_weight.set_text(
-      'The molecular weight is: <b>'+
-      calculated_weight?(_).to_s+'</b> Dalton'
+  def do_open_a_local_file(
+      this_widget = @parent_widget
     )
-    @label_molecular_weight.do_markify
-  end
-
-  # ========================================================================= #
-  # === set_main_entry
-  # ========================================================================= #
-  def set_main_entry(i)
-    @entry_input_sequence.set_text(i.to_s)
-  end; alias set_main_input_sequence set_main_entry # === set_main_input_sequence
-
-  # ========================================================================= #
-  # === set_main_input_sequence_and_evaluate_it
-  # ========================================================================= #
-  def set_main_input_sequence_and_evaluate_it(i)
-    simulate_enter_click(i)
-  end
-
-  # ========================================================================= #
-  # === main_entry?
-  # ========================================================================= #
-  def main_entry?
-    @entry_input_sequence
+    require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
+    widget = ::Gtk::SelectFile.new(this_widget) {{
+      current_folder:         ::Bioroebe.log_dir?,
+      additional_directories: ::Bioroebe.log_dir?
+    }}
+    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.
+      dataset = File.read(this_file)
+      set_main_entry(this_file.to_s)
+      fill_with_this(dataset.to_s)
+    end
+    return this_file
   end
 
   require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
@@ -195,30 +183,13 @@ class FormatConverter < ::Gtk::Box # === Bioroebe::GUI::Gtk::FormatConverter
       )
     else
       text = @combo_box.text?
-pp text
-pp text
-pp text
-pp _
-pp _
-pp _
       case text
       when 'to_fasta'
-pp File.read(_)
         result = Bioroebe.genbank_to_fasta(File.read(_))
-pp result
       end
     end
   end
 
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    @text_buffer = gtk_text_buffer
-    @text_view   = gtk_text_view(@text_buffer)
-    create_user_input
-  end
-
   # ========================================================================= #
   # === menu                                                       (menu tag)
   # ========================================================================= #
@@ -243,17 +214,43 @@ pp result
   end
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    @text_buffer = create_text_buffer
+    @text_view   = create_text_view(@text_buffer)
+    create_user_input
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
+  end
+
+  # ========================================================================= #
+  # === smaller_font?
+  # ========================================================================= #
+  def smaller_font?
+    SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
   # ========================================================================= #
-  def connect_skeleton
+  def connect_the_skeleton
     abort_on_exception
-    _ = gtk_left_aligned_label('Format Converter')
+
+    vbox = create_vbox
+    
+    _ = left_aligned_label('Format Converter')
     _.make_bold
-    minimal(_, 2)
+    vbox.minimal(_, 2)
     if first?
       @entry_input_sequence.set_text(first?.to_s)
     end
-    hbox = gtk_hbox
+    hbox = create_hbox
     hbox.maximal(@entry_input_sequence, 1)
     event_box = gtk_event_box(image_file_open)
     event_box.hint = 'Click on this button in order to '\
@@ -262,67 +259,141 @@ pp result
       do_open_a_local_file
     }
     hbox.minimal(event_box,       1)
-    add(hbox)
+    vbox.add(hbox)
     @entry_input_sequence.on_enter {
       simulate_enter_click
     }
-    hbox = gtk_hbox
+    hbox = create_hbox
     # ======================================================================= #
     # === button_do_convert
     # ======================================================================= #
-    button_do_convert = gtk_button('_Do convert')
+    button_do_convert = button('_Do convert', self, :use_mnemonics) {
+      :do_convert_the_file
+    }
     button_do_convert.remove_background
     button_do_convert.bblack1
     button_do_convert.pad6px
-    button_do_convert.on_clicked {
-      do_convert_the_file
-    }
     hbox.minimal(button_do_convert, 4)
-    @combo_box = gtk_combo_box(
+    @combo_box = create_combo_box(
       %w( to_fasta )
     )
     @combo_box.bblack1
     @combo_box.first_is_active
     hbox.minimal(@combo_box, 4)
-    minimal(hbox, 10)
-    scrolled_window = gtk_scrolled_window(@text_view) { :always }
-    scrolled_window.width_height(300, 600)
-    scrolled_window.bblack1
-    scrolled_window.css_class('pad2px')
-    minimal(scrolled_window, 2)
-    @label_n_aminoacids = left_aligned_text
-    minimal(@label_n_aminoacids, 2)
-    @label_molecular_weight = left_aligned_text
-    minimal(@label_molecular_weight, 2)
+    vbox.minimal(hbox, 10)
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << vbox
+
+    ::UniversalWidgets.set_main_window(window)
+    ::Bioroebe.cd(::Bioroebe.log_dir?)
+    menu
+    window.use_this_font = font?
+    window.show_all
+    window.set_padding(padding?)
+    window.set_border_size(border_size?)
+    window.set_size_request(width?, height?)
+    window.set_default_size(width?, height?)
+    window.top_left
+    run_main
   end
 
   # ========================================================================= #
-  # === do_open_a_local_file
+  # === create_user_input
   # ========================================================================= #
-  def do_open_a_local_file(
-      this_widget = @parent_widget
-    )
-    require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
-    widget = ::Gtk::SelectFile.new(this_widget) {{
-      current_folder:         ::Bioroebe.log_dir?,
-      additional_directories: ::Bioroebe.log_dir?
-    }}
-    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.
-      dataset = File.read(this_file)
-      set_main_entry(this_file.to_s)
-      fill_with_this(dataset.to_s)
+  def create_user_input
+    # ======================================================================= #
+    # === @entry_input_sequence
+    # ======================================================================= #
+    @entry_input_sequence = create_entry
+    @entry_input_sequence.hint = 'This will denote the current file.'
+    @entry_input_sequence.bblack1
+    @entry_input_sequence.yellow_background
+    @entry_input_sequence.pad5px
+  end
+
+  # ========================================================================= #
+  # === set_parent_widget
+  # ========================================================================= #
+  def set_parent_widget(i)
+    @parent_widget = i
+  end
+
+  # ========================================================================= #
+  # === fill_with_this
+  # ========================================================================= #
+  def fill_with_this(i)
+    @text_buffer.set_text(i)
+  end
+
+  # ========================================================================= #
+  # === calculated_weight?
+  # ========================================================================= #
+  def calculated_weight?(i)
+    this_file = Bioroebe.file_molecular_weight
+    dataset = YAML.load_file(this_file)
+    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
-    return this_file
+    # ======================================================================= #
+    # Must deduct water too.
+    # ======================================================================= #
+    weight -= (18.0 * (i.size - 1))
+    return weight.round(2)
   end
 
   # ========================================================================= #
-  # === run                                                         (run tag)
+  # === simulate_enter_click
   # ========================================================================= #
-  def run
-     ::Bioroebe.cd(::Bioroebe.log_dir?) 
-    create_skeleton_then_connect_skeleton
-    menu
+  def simulate_enter_click(
+      _ = @entry_input_sequence.text?
+    )
+    _.upcase!
+    _ = ::Bioroebe.filter_away_invalid_aminoacids(_)
+    @entry_input_sequence.set_text(_)
+    fill_the_table_data_with_this_sequence(_)
+    @label_n_aminoacids.set_text(
+      "This sequence has <b>#{_.size}</b> aminoacids."
+    )
+    @label_n_aminoacids.do_markify
+    @label_molecular_weight.set_text(
+      'The molecular weight is: <b>'+
+      calculated_weight?(_).to_s+'</b> Dalton'
+    )
+    @label_molecular_weight.do_markify
+  end
+
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_input_sequence.set_text(i.to_s)
+  end; alias set_main_input_sequence set_main_entry # === set_main_input_sequence
+
+  # ========================================================================= #
+  # === set_main_input_sequence_and_evaluate_it
+  # ========================================================================= #
+  def set_main_input_sequence_and_evaluate_it(i)
+    simulate_enter_click(i)
+  end
+
+  # ========================================================================= #
+  # === main_entry?
+  # ========================================================================= #
+  def main_entry?
+    @entry_input_sequence
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::FormatConverter[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
   end
 
   # ========================================================================= #
@@ -331,15 +402,16 @@ pp result
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::FormatConverter.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_top_left_then_run
-  end
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::FormatConverter.new(i)
+    )
+    r.background_colour(:white)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::FormatConverter.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::FormatConverter.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::FormatConverter.run
+  Bioroebe::GUI::UniversalWidgets::FormatConverter.new(ARGV)
 end # gtkformatconverter