bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/{shared_code/show_codon_usage/show_codon_usage_module.rb → universal_widgets/show_codon_usage/show_codon_usage.rb}

@@ -2,36 +2,69 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::ShowCodonUsageModule
+# === Bioroebe::GUI::UniversalWidgets::ShowCodonUsage
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::ShowCodonUsage.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb'
-# include Bioroebe::GUI::ShowCodonUsageModule
+# require 'bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb'
 # =========================================================================== #
+require 'universal_widgets/base/base.rb'
+
 module Bioroebe
 
 module GUI
 
-module ShowCodonUsageModule 
+module UniversalWidgets
 
-  require 'bioroebe/codons/show_codon_usage.rb'
-  require 'bioroebe/toplevel_methods/remove.rb'
+class ShowCodonUsage < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::ShowCodonUsage
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
 
-  alias e puts
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/codons/show_codon_usage.rb'
 
   # ========================================================================= #
   # === TITLE
+  #
+  # Specify which title to use for this small widget.
   # ========================================================================= #
   TITLE = 'Show Codon Usage'
 
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH = '65% or minimum 600px'
+  WIDTH = '65% or 600px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = '50%'
+  HEIGHT = '55% or 400px minimum'
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
 
   # ========================================================================= #
   # === TEST_SEQUENCE
@@ -39,14 +72,37 @@ module ShowCodonUsageModule
   TEST_SEQUENCE = 'AGACGTACGTACGTCAGTCAGTACGTACTGATCGTAGCTAGCTACGTGACC'
 
   # ========================================================================= #
-  # === USE_THIS_FONT
+  # === initialize
   # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_20
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    determine_the_GUI_to_be_used(commandline_arguments)
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
 
   # ========================================================================= #
-  # === reset_the_shared_module
+  # === reset                                                     (reset tag)
   # ========================================================================= #
-  def reset_the_shared_module
+  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 if use_gtk3?
     # ======================================================================= #
     # === @use_this_as_the_input_sequence
     #
@@ -67,7 +123,49 @@ module ShowCodonUsageModule
   # === border_size?
   # ========================================================================= #
   def border_size?
-    4
+    2
+  end
+  # ========================================================================= #
+  # === create_box_top_five_codons
+  # ========================================================================= #
+  def create_box_top_five_codons
+    @box_top_five_codons = create_vbox
+    @box_top_five_codons.set_font(:hack_20)
+  end
+
+  # ========================================================================= #
+  # === create_the_label_top_five_codons
+  # ========================================================================= #
+  def create_the_label_top_five_codons
+    @label_top_five_codons = label
+  end
+
+  # ========================================================================= #
+  # === create_the_label_showing_n_nucleotides
+  # ========================================================================= #
+  def create_the_label_showing_n_nucleotides
+    @label_showing_n_nucleotides = label
+    @label_showing_n_nucleotides.set_font('Bitstream Vera Sans 22')
+  end
+
+  # ========================================================================= #
+  # === create_the_main_entry                                     (entry tag)
+  # ========================================================================= #
+  def create_the_main_entry
+    # ======================================================================= #
+    # === @entry1
+    # ======================================================================= #
+    @entry1 = create_entry
+    @entry1.set_text(@use_this_as_the_input_sequence)
+    @entry1.set_font(:hack_20)
+    @entry1.hint =
+      "This entry should contain the nucleotide sequence that "\
+      "the user wants to analyse. \n\nAs soon as the user has "\
+      "finished the sequence, the '<b>enter</b>' key can be used "\
+      "to analyse the sequence."
+    @entry1.on_enter {
+      do_the_conversion_then_update_the_label_as_well
+    } if @entry1.respond_to? :on_enter
   end
 
   # ========================================================================= #
@@ -139,6 +237,7 @@ module ShowCodonUsageModule
     @label_top_five_codons.set_text(
       text_for_the_label
     )
+    @label_top_five_codons.make_selectable
     @label_top_five_codons.do_markify # Apply any markup rules here.
     @text_view.set_text(_.strip)
   end
@@ -146,7 +245,9 @@ module ShowCodonUsageModule
   # ========================================================================= #
   # === handle_the_commandline_arguments
   # ========================================================================= #
-  def handle_the_commandline_arguments(i = @commandline_arguments)
+  def handle_the_commandline_arguments(
+      i = commandline_arguments?
+    )
     i.each {|entry|
       if File.file? entry
         @use_this_as_the_input_sequence = File.read(entry).
@@ -157,57 +258,137 @@ module ShowCodonUsageModule
   end
 
   # ========================================================================= #
-  # === create_box_top_five_codons
+  # === main_font?
   # ========================================================================= #
-  def create_box_top_five_codons
-    if use_gtk3?
-      @box_top_five_codons = gtk_box # This is a Gtk::Box. It will contain @label_top_five_codons.
-    else
-      @box_top_five_codons = padded_vbox
-    end
-    @box_top_five_codons.set_font(:hack_20)
+  def main_font?
+    USE_THIS_FONT
   end
 
   # ========================================================================= #
-  # === create_the_label_top_five_codons
+  # === slightly_smaller_font?
   # ========================================================================= #
-  def create_the_label_top_five_codons
-    @label_top_five_codons = label
+  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_scrolled_window                             (scrolled tag)
+  # ========================================================================= #
+  def create_the_scrolled_window
+    # ======================================================================= #
+    # === @scrolled_window
+    # ======================================================================= #
+    @scrolled_window = create_scrolled_window(@text_view) { :only_top_and_bottom_scrollbar }
+    @scrolled_window.set_font(:hack_20)
+    @scrolled_window.read_only
+    @scrolled_window.pad8px
+    @scrolled_window.set_border_width(5)
+    @scrolled_window.set_size_request(550, 300)
+  end
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    create_the_label_showing_n_nucleotides
+    create_the_main_entry
+    create_the_label_top_five_codons
+    create_the_text_view # Must be created before the scrolled window.
+    create_the_scrolled_window
   end
 
   # ========================================================================= #
   # === create_the_text_view
   # ========================================================================= #
   def create_the_text_view
-    @text_view = text_view
+    @text_view = create_text_view
   end
 
   # ========================================================================= #
-  # === create_the_label_showing_n_nucleotides
+  # === run                                                         (run tag)
   # ========================================================================= #
-  def create_the_label_showing_n_nucleotides
-    @label_showing_n_nucleotides = label
-    @label_showing_n_nucleotides.set_font('Bitstream Vera Sans 22')
+  def run
+    run_super
   end
 
   # ========================================================================= #
-  # === create_the_main_entry                                     (entry tag)
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
   # ========================================================================= #
-  def create_the_main_entry
-    # ======================================================================= #
-    # === @entry1
-    # ======================================================================= #
-    @entry1 = entry
-    @entry1.set_text(@use_this_as_the_input_sequence)
-    @entry1.set_font(:hack_20)
-    @entry1.hint =
-      "This entry should contain the nucleotide sequence that "\
-      "the user wants to analyse. \n\nAs soon as the user has "\
-      "finished the sequence, the '<b>enter</b>' key can be used "\
-      "to analyse the sequence."
-    @entry1.on_enter {
+  def connect_the_skeleton
+    abort_on_exception
+
+    vbox = create_vbox
+
+    handle_the_commandline_arguments
+    vbox.minimal(@entry1)
+    update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence
+    vbox.minimal(@label_showing_n_nucleotides)
+    vbox.minimal(hspacer)
+    create_box_top_five_codons
+    @box_top_five_codons.minimal(@label_top_five_codons, 10)
+    draggable_pane = gtk_drag_top_to_bottom(
+      @scrolled_window,
+      @box_top_five_codons
+    )
+    vbox.maximal(draggable_pane)
+
+    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?)
+    handle_the_commandline_arguments # This must come after the GUI skeleton was created.
+    Thread.new {
+      sleep 0.02
       do_the_conversion_then_update_the_label_as_well
-    } if @entry1.respond_to? :on_enter
+      @entry1.deselect
+    }
+    window.top_left
+    run_main
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::ShowCodonUsage[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
   end
 
-end; end; end
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::ShowCodonUsage.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::ShowCodonUsage.new(i)
+    )
+    r.modify_background(:normal, :mintcream)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::ShowCodonUsage.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::ShowCodonUsage.start_gui_application
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::UniversalWidgets::ShowCodonUsage.new(ARGV)
+end # gtkshowcodonusage

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

@@ -2,59 +2,91 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::Sizeseq
+# === Bioroebe::GUI::UniversalWidgets::Sizeseq
+#
+# This is, I believe, incomplete - missing some way to do the actual
+# sizeseq-comparison.
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::Sizeseq.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/sizeseq/sizeseq.rb'
-# Bioroebe::GUI::Gtk::Sizeseq.run
+# require 'bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb'
 # =========================================================================== #
-require 'gtk_paradise/require_gtk3'
+require 'universal_widgets/base/base.rb'
 
 module Bioroebe
 
 module GUI
 
-module Gtk
+module UniversalWidgets
 
-class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq 
+class Sizeseq < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::Sizeseq
 
-  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.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/fasta_and_fastq/parse_fasta/parse_fasta.rb'
 
   # ========================================================================= #
   # === TITLE
+  #
+  # Specify which title to use for this small widget.
   # ========================================================================= #
   TITLE = 'Sizeseq'
 
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH = '80% or minimum 800px'
+  WIDTH = '75% or 800px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = 500
+  HEIGHT = '55% or 500px minimum'
+
+  # ========================================================================= #
+  # === TEXT_COMPARE_THE_TWO_SEQUENCES
+  # ========================================================================= #
+  TEXT_COMPARE_THE_TWO_SEQUENCES = '_Compare the two sequences'
 
   # ========================================================================= #
-  # === USE_THIS_FONT
+  # === MONOSPACED_FONT
+  #
+  # When this font is changed, don't forget to also change the font
+  # at SMALLER_FONT.
   # ========================================================================= #
-  USE_THIS_FONT = :hack_16
+  MONOSPACED_FONT = :hack_20
+    USE_THIS_FONT = MONOSPACED_FONT
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === PADDING_TO_USE
+  # ========================================================================= #
+  PADDING_TO_USE = 4
 
   # ========================================================================= #
   # === 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
@@ -66,26 +98,34 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
   # === 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?
     # ======================================================================= #
     # === @use_this_file
     # ======================================================================= #
-    @use_this_file = ::Bioroebe.project_base_directory?+'data/fasta/GFP_mutant_3_coding_sequence.fasta'
+    @use_this_file = ::Bioroebe.project_base_directory?+
+                     'data/fasta/GFP_mutant_3_coding_sequence.fasta'
+    unless File.exist? @use_this_file
+      @use_this_file = '/home/x/programming/ruby/src/bioroebe/lib/bioroebe/data/fasta/GFP_mutant_3_coding_sequence.fasta'
+    end
   end
 
   # ========================================================================= #
   # === padding?
   # ========================================================================= #
   def padding?
-    4
+    PADDING_TO_USE
   end
 
   # ========================================================================= #
@@ -96,9 +136,76 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
   end
 
   # ========================================================================= #
-  # === create_skeleton                                          (create tag)
+  # === main_font?
   # ========================================================================= #
-  def create_skeleton
+  def main_font?
+    USE_THIS_FONT
+  end
+
+  # ========================================================================= #
+  # === slightly_smaller_font?
+  # ========================================================================= #
+  def slightly_smaller_font?
+    USE_THIS_SLIGHTLY_SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === handle_CSS_rules                                   (CSS tag, css tag)
+  # ========================================================================= #
+  def handle_CSS_rules
+    use_gtk_paradise_project_css_file
+    append_project_css_file
+    add_these_custom_CSS_rules '
+'
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+
+    result = ::Bioroebe.return_sizeseq(@use_this_file)
+    @textview = create_textview
+    @textview.set_text(result)
+    scrolled_window = create_scrolled_window(@textview) { :always }
+    scrolled_window.bblack2
+    scrolled_window.set_size_request(1000, 600)
+    # ======================================================================= #
+    # Next, create our main vbox.
+    # ======================================================================= #
+    vbox = create_vbox
+    vbox.minimal(return_widget_containing_the_top_bar, 4)
+    vbox.minimal(scrolled_window, 4)
+    vbox.minimal(return_widget_containing_the_filepath)
+
+    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.set_size_request(80, 100)
+    window.top_left
+    run_main
   end
 
   # ========================================================================= #
@@ -106,11 +213,10 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
   # ========================================================================= #
   def return_widget_containing_the_top_bar
     _ = default_top_bar
-    button_open_file = gtk_button('Open file')
+    button_open_file = button('_Open file', self, :use_mnemonics) {
+      :do_open_a_file if use_gtk3?
+    } 
     button_open_file.bblack1
-    button_open_file.on_clicked {
-      do_open_a_file
-    }
     _.add(button_open_file)
     return _
   end
@@ -144,9 +250,9 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
   # === return_widget_containing_the_filepath
   # ========================================================================= #
   def return_widget_containing_the_filepath
-    vbox = gtk_vbox
+    vbox = create_vbox
     vbox << text('Use this file:')
-    @entry_use_this_file = gtk_entry
+    @entry_use_this_file = create_entry
     @entry_use_this_file.yellow_background
     @entry_use_this_file.center_align
     vbox.minimal(@entry_use_this_file, 1)
@@ -155,35 +261,10 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
   end
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === Bioroebe::GUI::UniversalWidgets::Sizeseq[]
   # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    result = ::Bioroebe.return_sizeseq(@use_this_file)
-    @textview = gtk_textview
-    @textview.set_text(result)
-    scrolled_window = gtk_scrolled_window(@textview) { :always }
-    scrolled_window.bblack2
-    scrolled_window.set_size_request(1000, 600)
-    # ======================================================================= #
-    # Next, create our main vbox.
-    # ======================================================================= #
-    vbox = gtk_vbox
-    vbox.minimal(return_widget_containing_the_top_bar, 4)
-    vbox.minimal(scrolled_window, 4)
-    vbox.minimal(return_widget_containing_the_filepath)
-    if respond_to? :set_title
-      set_title(' Compare different FASTA sequences ')
-    end
-    set_border_width(2)
-    add(vbox)
-  end
-
-  # ========================================================================= #
-  # === run                                                         (run tag)
-  # ========================================================================= #
-  def run
-    create_skeleton_then_connect_skeleton
+  def self.[](i = ARGV)
+    new(i)
   end
 
   # ========================================================================= #
@@ -192,15 +273,16 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::Sizeseq.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_top_left_then_run
-  end
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::Sizeseq.new(i)
+    )
+    r.modify_background(:normal, :mintcream)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::Sizeseq.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::Sizeseq.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::Sizeseq.run
-end
+  Bioroebe::GUI::UniversalWidgets::Sizeseq.new(ARGV)
+end # gtkproteintodna