bioroebe 0.12.24 → 0.13.31

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

@@ -2,61 +2,101 @@
 # Encoding: UTF-8
 # frozen_string_literal: true
 # =========================================================================== #
-# === Bioroebe::GUI::Gtk::ParsePdbFile
+# === Bioroebe::GUI::UniversalWidgets::ParsePdbFile
+##
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::ParsePdbFile.new(ARGV)
+#
 # =========================================================================== #
-# require 'bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb'
-# Bioroebe::GUI::Gtk::ParsePdbFile.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 ParsePdbFile < ::Gtk::Frame # === Bioroebe::GUI::Gtk::ParsePdbFile 
+class ParsePdbFile < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::ParsePdbFile
 
-  require 'bioroebe/pdb/parse_pdb_file.rb'
-  require 'bioroebe/toplevel_methods/file_and_directory_related_actions.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/pdb_and_protein_structure/parse_pdb_file.rb'
 
   # ========================================================================= #
   # === TITLE
+  #
+  # Specify which title to use for this widget.
   # ========================================================================= #
   TITLE = ' Parse a .pdb file '
 
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH = 1200
+  WIDTH = '75% or 1200px minimum'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = 500
+  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_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
 
   # ========================================================================= #
-  # === USE_THIS_FONT
+  # === USE_THIS_HEADER
   # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_22
+  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(" #{TITLE} ")
-    make_bold
+    determine_the_GUI_to_be_used(commandline_arguments)
     reset
     set_commandline_arguments(
       commandline_arguments
@@ -68,17 +108,21 @@ class ParsePdbFile < ::Gtk::Frame # === Bioroebe::GUI::Gtk::ParsePdbFile
   # === 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
-
+  
   # ========================================================================= #
   # === padding?
   # ========================================================================= #
@@ -94,124 +138,44 @@ class ParsePdbFile < ::Gtk::Frame # === Bioroebe::GUI::Gtk::ParsePdbFile
   end
 
   # ========================================================================= #
-  # === create_the_scrolled_window_containing_the_aminoacid_sequence
+  # === main_font?
   # ========================================================================= #
-  def create_the_scrolled_window_containing_the_aminoacid_sequence
-    @text_buffer = gtk_text_buffer
-    @text_view = gtk_text_view(@text_buffer)
-    @scrolled_window = gtk_scrolled_window(@text_view) { :left_right }
-    @scrolled_window.clear_background
-    @scrolled_window.css_class('royalblue')
-    @scrolled_window.bblack1
-    @scrolled_window.width_height(400, 50)
-    @scrolled_window.set_name('differently_coloured_selection')
+  def main_font?
+    USE_THIS_FONT
   end
 
   # ========================================================================= #
-  # === create_skeleton                                          (create tag)
+  # === slightly_smaller_font?
   # ========================================================================= #
-  def create_skeleton
-    create_the_scrolled_window_containing_the_aminoacid_sequence
+  def slightly_smaller_font?
+    USE_THIS_SLIGHTLY_SMALLER_FONT
   end
 
   # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
+  # === handle_CSS_rules                                   (CSS tag, css tag)
   # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    @outer_vbox = gtk_vbox
-    @outer_vbox.set_border_width(18)
-    _ = first_argument?.to_s
-    if _.start_with? '--'
-      _ = '' # In this case ignore it.
-    end
-    if File.exist? _
-    else
-      ::Bioroebe.no_file_exists_at(_)
-    end
-    @dataset = ::Bioroebe::ParsePdbFile.new(_) { :be_silent }
-    hbox = gtk_hbox
-    hbox.minimal(text('File name: '))
-    @file_name = text_bold(File.absolute_path(_))
-    hbox.minimal(@file_name)
-    hbox.minimal(return_widget_containing_a_file_open_button, 9)
-    @outer_vbox.minimal(hbox, 8)
-    @outer_vbox.minimal(gtk_horizontal_spacer, 2)
-    hbox = gtk_hbox
-    @label_the_name_of_the_organism = text(
-      'The name of the organism (Entry: '+
-      '<span weight="bold" color="steelblue">ORGANISM_SCIENTIFIC</span>'+
-      +') is'
-    )
-    @label_the_name_of_the_organism.do_markify
-    hbox.minimal(@label_the_name_of_the_organism, 5)
-    @outer_vbox.add(hbox)
-    if @dataset
-      taxid = @dataset.taxid_of_the_species?.to_s
-      @label_taxid = text(
-        '<span weight="bold" color="indigo">'+@dataset.name_of_the_species?.to_s+
-        '</span>'+
-        ' (Taxid: ➡️ '+
-        '<span weight="bold"><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+taxid+'">'+
-        taxid+'</a></span>; '+@dataset.organism_common?.to_s+')'
-      )
-      @label_taxid.make_selectable
-      @label_taxid.do_markify
-      @outer_vbox.add(hbox(@label_taxid))
-    end
-    add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
-    add_the_aminoacid_sequence
-    add_how_many_alpha_helices_can_be_found_in_this_protein
-    add_the_maximum_difference_between_the_atoms
-    add(@outer_vbox)
-    set_border_width(5)
-  end
-
-  # ========================================================================= #
-  # === add_the_maximum_difference_between_the_atoms
-  # ========================================================================= #
-  def add_the_maximum_difference_between_the_atoms
-    _ = gtk_hbox
-    if @dataset
-      text = left_aligned_text(
-               'The maximum difference between the atoms is <b>'+
-               @dataset.max_distance?.to_s.to_f.round(3).to_s+'</b>.'
-             )
-      text.make_selectable
-      _ << text
-    end
-    @outer_vbox.add(_)
-  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
 
   # ========================================================================= #
-  # === add_the_aminoacid_sequence
+  # === add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
   # ========================================================================= #
-  def add_the_aminoacid_sequence
-    _ = gtk_vbox
-    @text_for_the_aminoacid_sequence = left_aligned_text(
-      'The aminoacid sequence (<b>'+@dataset.n_aminoacids?.to_s+
-      '</b> aminoacids) is:'
+  def add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
+    _ = create_hbox
+    text = left_aligned_text(
+      "\n<b>#{@dataset.n_atom_entries?.to_s}"\
+      "</b> ATOM entries were found being part of this file."
     )
-    @text_for_the_aminoacid_sequence.make_selectable
-    _.minimal(@text_for_the_aminoacid_sequence, 10)
-    update_the_scrolled_window_with_the_current_aminoacid_sequence
-    _.minimal(@scrolled_window, 15)
+    text.make_selectable
+    _ << text
     @outer_vbox.add(_)
   end
 
-  # ========================================================================= #
-  # === add_how_many_alpha_helices_can_be_found_in_this_protein
-  # ========================================================================= #
-  def add_how_many_alpha_helices_can_be_found_in_this_protein
-    _ = gtk_hbox
-    @label_protein_contans_n_alpha_helices = left_aligned_text('This protein contains <b>'+
-         @dataset.n_alpha_helices?.to_s+
-         '</b> alpha-helices.')
-    @label_protein_contans_n_alpha_helices.make_selectable
-    _ << @label_protein_contans_n_alpha_helices
-    @outer_vbox.minimal(_, 2)
-  end
-
   # ========================================================================= #
   # === update_the_aminoacid_sequence_is_label
   # ========================================================================= #
@@ -279,7 +243,7 @@ class ParsePdbFile < ::Gtk::Frame # === Bioroebe::GUI::Gtk::ParsePdbFile
   # This is the widget with the "open file" functionality.
   # ========================================================================= #
   def return_widget_containing_a_file_open_button
-    button_open_file = gtk_file_open_button
+    button_open_file = file_open_button
     button_open_file.bblack1
     button_open_file.on_click {
       create_a_new_file_chooser_dialog(
@@ -301,24 +265,176 @@ class ParsePdbFile < ::Gtk::Frame # === Bioroebe::GUI::Gtk::ParsePdbFile
   end
 
   # ========================================================================= #
-  # === add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
+  # === add_how_many_alpha_helices_can_be_found_in_this_protein
   # ========================================================================= #
-  def add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
-    _ = gtk_hbox
-    text = left_aligned_text(
-      "\n<b>#{@dataset.n_atom_entries?.to_s}"\
-      "</b> ATOM entries were found being part of this file."
-    )
-    text.make_selectable
-    _ << text
-    @outer_vbox.add(_)
+  def add_how_many_alpha_helices_can_be_found_in_this_protein
+    _ = create_hbox
+    @label_protein_contans_n_alpha_helices = left_aligned_text('This protein contains <b>'+
+         @dataset.n_alpha_helices?.to_s+
+         '</b> alpha-helices.')
+    @label_protein_contans_n_alpha_helices.make_selectable
+    _ << @label_protein_contans_n_alpha_helices
+    @outer_vbox.minimal(_, 2)
+  end
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    create_the_scrolled_window_containing_the_aminoacid_sequence
   end
 
   # ========================================================================= #
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
-    create_skeleton_then_connect_skeleton
+    run_super
+  end
+
+  # ========================================================================= #
+  # === smaller_font?
+  # ========================================================================= #
+  def smaller_font?
+    SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+    
+    @outer_vbox = create_vbox
+    @outer_vbox.set_border_width(18)
+    _ = first_argument?.to_s
+    if _.start_with? '--'
+      _ = '' # In this case ignore it.
+    end
+    if File.exist? _
+    else
+      ::Bioroebe.no_file_exists_at(_)
+    end
+    @dataset = ::Bioroebe::ParsePdbFile.new(_) { :be_silent }
+    hbox = create_hbox
+    hbox.minimal(
+      text('File name: ')
+    )
+    @file_name = bold_text(File.absolute_path(_))
+
+    @file_name.make_selectable
+    hbox.minimal(@file_name)
+    hbox.minimal(return_widget_containing_a_file_open_button, 9)
+    @outer_vbox.minimal(hbox, 8)
+    @outer_vbox.minimal(horizontal_spacer, 2)
+    hbox = create_hbox
+    @label_the_name_of_the_organism = text(
+      'The name of the organism (Entry: '+
+      '<span weight="bold" color="steelblue">ORGANISM_SCIENTIFIC</span>'+
+      +') is'
+    )
+    @label_the_name_of_the_organism.make_selectable
+    @label_the_name_of_the_organism.do_markify
+    hbox.minimal(@label_the_name_of_the_organism, 5)
+    @outer_vbox.add(hbox)
+    if @dataset
+      taxid = @dataset.taxid_of_the_species?.to_s
+      @label_taxid = text(
+        '<span weight="bold" color="indigo">'+@dataset.name_of_the_species?.to_s+
+        '</span>'+
+        ' (Taxid: ➡️ '+
+        '<span weight="bold"><a href="https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?id='+taxid+'">'+
+        taxid+'</a></span>; '+@dataset.organism_common?.to_s+')'
+      )
+      @label_taxid.make_selectable
+      @label_taxid.do_markify
+      @outer_vbox.add(hbox(@label_taxid))
+    end
+    add_information_about_how_many_atom_entries_are_part_of_that_pdb_file
+    add_the_aminoacid_sequence
+    add_how_many_alpha_helices_can_be_found_in_this_protein
+    add_the_maximum_difference_between_the_atoms
+
+    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?)
+    jump_into_the_first_entry
+    window.top_left
+    run_main
+  end
+
+  # ========================================================================= #
+  # === jump_into_the_first_entry
+  # ========================================================================= #
+  def jump_into_the_first_entry
+    entry1?.do_focus
+  end
+
+  # ========================================================================= #
+  # === add_the_maximum_difference_between_the_atoms
+  # ========================================================================= #
+  def add_the_maximum_difference_between_the_atoms
+    _ = create_hbox
+    if @dataset
+      text = left_aligned_text(
+               'The maximum difference between the atoms is <b>'+
+               @dataset.max_distance?.to_s.to_f.round(3).to_s+'</b>.'
+             )
+      text.make_selectable
+      _ << text
+    end
+    @outer_vbox.add(_)
+  end
+
+  # ========================================================================= #
+  # === add_the_aminoacid_sequence
+  # ========================================================================= #
+  def add_the_aminoacid_sequence
+    _ = create_vbox
+    @text_for_the_aminoacid_sequence = left_aligned_text(
+      'The aminoacid sequence (<b>'+@dataset.n_aminoacids?.to_s+
+      '</b> aminoacids) is:'
+    )
+    @text_for_the_aminoacid_sequence.make_selectable
+    _.minimal(@text_for_the_aminoacid_sequence, 10)
+    update_the_scrolled_window_with_the_current_aminoacid_sequence
+    _.minimal(@scrolled_window, 15)
+    @outer_vbox.add(_)
+  end
+
+  # ========================================================================= #
+  # === create_the_scrolled_window_containing_the_aminoacid_sequence
+  # ========================================================================= #
+  def create_the_scrolled_window_containing_the_aminoacid_sequence
+    @text_buffer = create_text_buffer
+    @text_view = create_text_view(@text_buffer)
+    @scrolled_window = create_scrolled_window(@text_view) { :left_right }
+    @scrolled_window.clear_background
+    @scrolled_window.css_class('royalblue')
+    @scrolled_window.bblack1
+    @scrolled_window.width_height(400, 50)
+    @scrolled_window.set_name('differently_coloured_selection')
+  end
+
+  # ========================================================================= #
+  # === scrolled_window?
+  # ========================================================================= #
+  def scrolled_window?
+    @scrolled_window
+  end; alias entry1? scrolled_window? # === entry1?
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::ParsePdbFile[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
   end
 
   # ========================================================================= #
@@ -327,16 +443,16 @@ class ParsePdbFile < ::Gtk::Frame # === Bioroebe::GUI::Gtk::ParsePdbFile
   def self.run(
       i = ARGV
     )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::ParsePdbFile.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_size_then_automatic_title
-    r.middle_then_run
-  end
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::ParsePdbFile.new(i)
+    )
+    r.background_colour(:white)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::ParsePdbFile.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::ParsePdbFile.start_gui_application
 
 end; end; end; end
 
 if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::Gtk::ParsePdbFile.run
-end # gtk_parse_pdb_file
+  Bioroebe::GUI::UniversalWidgets::ParsePdbFile.new(ARGV)
+end # gtkparsepdbfile