bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb

@@ -0,0 +1,408 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::UniversalWidgets::AminoacidComposition
+#
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::AminoacidComposition.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/universal_widgets/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria.rb'
+# =========================================================================== #
+require 'universal_widgets/base/base.rb'
+
+module Bioroebe
+
+module GUI
+
+module UniversalWidgets
+
+class AminoacidComposition < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::AminoacidComposition
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
+
+  require 'bioroebe/conversions/convert_aminoacid_to_dna.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = ' Protein-to-DNA conversion '
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '65% or 500px minimum'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '55% or 300px minimum'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :hack_26
+
+  # ========================================================================= #
+  # === USE_THIS_SLIGHTLY_SMALLER_FONT
+  # ========================================================================= #
+  USE_THIS_SLIGHTLY_SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === USE_THIS_TITLE_FOR_THE_MAIN_BUTTON
+  # ========================================================================= #
+  USE_THIS_TITLE_FOR_THE_MAIN_BUTTON = '_Determine the DNA sequence'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  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                                                     (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?]
+    # ======================================================================= #
+    # === 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?
+    set_label_widget(
+      create_label.set_markup(
+        %Q(<span foreground="#000000" weight="bold">#{TITLE}</span>)
+      )
+    ) if respond_to?(:set_label_widget) and use_gtk3? # Do this after handle_CSS().
+    # ======================================================================= #
+    # === @dataset
+    # ======================================================================= #
+    @dataset = {}
+  end
+
+  # ========================================================================= #
+  # === create_right_buffer
+  # ========================================================================= #
+  def create_right_buffer
+    # ======================================================================= #
+    # === :right_buffer
+    # ======================================================================= #
+    @dataset[:right_buffer] = create_text_view # The right text view.
+    @dataset[:right_buffer].bblack1
+    @dataset[:right_buffer].do_wrap_properly
+  end
+
+  # ========================================================================= #
+  # === create_middle_bar_containing_the_arrow_pointing_to_the_right_side
+  # ========================================================================= #
+  def create_middle_bar_containing_the_arrow_pointing_to_the_right_side
+    @middle_bar = create_vbox
+    event_box = create_eventbox(
+      create_label(:arrow_right)
+    )
+    event_box.hint =
+      'This arrow can be clicked, to convert from the aminoacid sequence '\
+      'to (one likely) possible DNA sequence.'
+    event_box.on_clicked {
+      do_determine_the_backtrack_sequence
+    }
+    @middle_bar.minimal(
+      event_box
+    )
+  end
+
+  # ========================================================================= #
+  # === create_top_hbox
+  # ========================================================================= #
+  def create_top_hbox
+    # ======================================================================= #
+    # The paned-widget is close to the top.
+    # ======================================================================= #
+    scrolled_window_right = scrolled_window(right_buffer?)
+    scrolled_window_right.clear_background
+    scrolled_window_right.width_height(300, 300)
+    scrolled_window_right.bblack1
+    scrolled_window_right.mar2px
+    # ======================================================================= #
+    # === scrolled_window_left
+    # ======================================================================= #
+    scrolled_window_left  = scrolled_window(left_buffer?)
+    scrolled_window_left.clear_background
+    scrolled_window_left.width_height(300, 300)
+    scrolled_window_left.bblack1
+    scrolled_window_left.mar2px
+    top_hpaned = gtk_hpaned(
+      scrolled_window_left,
+      scrolled_window_right
+    ) {{ border_width: 10 }}
+    this_position = (width?.to_f / 1.5).to_i
+    top_hpaned.set_position(this_position)
+    top_hpaned.show_all
+    @dataset[:top_hbox] = top_hpaned
+  end
+
+  # ========================================================================= #
+  # === create_left_buffer
+  # ========================================================================= #
+  def create_left_buffer
+    # ======================================================================= #
+    # === :left_buffer
+    # ======================================================================= #
+    @dataset[:left_buffer] = create_text_view # The left text view.
+    @dataset[:left_buffer].bblack1
+    @dataset[:left_buffer].do_wrap_properly
+  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
+    add_these_custom_CSS_rules '
+
+#custom_treeview.view header button {
+  background-color: white;
+  color: royalblue;
+  font-weight: bold;
+  font-size: larger;
+  padding: 8px;
+}'
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === menu                                                         (menu tag)
+  # ========================================================================= #
+  def menu(i = nil)
+    if i
+      if i.is_a? Array
+        i.each {|entry| menu(entry) }
+      else
+        case i # case tag
+        when ''
+        end
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    2
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    0
+  end
+
+  # ========================================================================= #
+  # === create_buttons                                            (buttons tag)
+  # ========================================================================= #
+  def create_buttons
+    backtrack_button = bold_button(
+      USE_THIS_TITLE_FOR_THE_MAIN_BUTTON, self, :use_mnemonic
+    ) {
+      :do_determine_the_backtrack_sequence
+    }
+    backtrack_button.set_name('button1')
+    backtrack_button.do_use_underline
+    backtrack_button.hint = 
+      "On the <b>left hand side</b>, you should input the "\
+      "Aminoacid sequence.\n\n"\
+      "On the <b>right hand side</b>, a possible DNA "\
+      "sequence for this Aminoacid Sequence will "\
+      "be displayed.\n\n"\
+      "Invalid amino acids, such as 'U', will be filtered "\
+      "out, if given.\n\n"\
+      "Note that this will not necessarily "\
+      "generate the same sequence, due to several different codons "\
+      "encoding for the same aminoacid."
+    backtrack_button.on_hover_lightblue
+    @dataset[:backtrack_button] = backtrack_button
+    a_quit_button = quit_button
+    a_quit_button.set_name('button1')
+    a_quit_button.make_bold
+    @dataset[:quit_button] = a_quit_button
+  end
+
+  # ========================================================================= #
+  # === filter_away_invalid_aminoacids_from_the_left_buffer
+  #
+  # This method is used to "sanitize" the input - invalid aminoacids
+  # are flat out removed.
+  # ========================================================================= #
+  def filter_away_invalid_aminoacids_from_the_left_buffer
+    _ = left_buffer?.text?.to_s
+    possible_new_text = Bioroebe.strict_filter_away_invalid_aminoacids(_)
+    unless _ == possible_new_text
+      left_buffer?.set_text(possible_new_text)
+    end
+  end
+
+  # ========================================================================= #
+  # === right_buffer?
+  # ========================================================================= #
+  def right_buffer?
+    @dataset[:right_buffer]
+  end; alias right? right_buffer? # === right?
+
+  # ========================================================================= #
+  # === set_aminoacid_sequence
+  # ========================================================================= #
+  def set_aminoacid_sequence(i)
+    @dataset[:left_buffer].set_text(i.to_s)
+  end
+
+  # ========================================================================= #
+  # === aminoacid_sequence?
+  # ========================================================================= #
+  def aminoacid_sequence?
+    left_buffer?.to_s
+  end
+
+  # ========================================================================= #
+  # === left_buffer?
+  # ========================================================================= #
+  def left_buffer?
+    @dataset[:left_buffer]
+  end; alias left? left_buffer? # === left?
+
+  # ========================================================================= #
+  # === do_determine_the_backtrack_sequence                           (click tag)
+  #
+  # This will do what is necessary to find the backtrack sequence.
+  # ========================================================================= #
+  def do_determine_the_backtrack_sequence
+    filter_away_invalid_aminoacids_from_the_left_buffer
+    _ = left_buffer?.text?.to_s
+    _.upcase!
+    _ = ::Bioroebe.remove_invalid_aminoacids(_)
+    left_buffer?.set_text(_)
+    # ======================================================================= #
+    # Ok, now we can determine the right hand side:
+    # ======================================================================= #
+    text_for_right_hand_side = ::Bioroebe::ProteinToDNA.new(_, :be_quiet).dna_sequence?
+    right_buffer?.set_text(text_for_right_hand_side)
+  end; alias do_determine_the_DNA_sequence do_determine_the_backtrack_sequence # === do_determine_the_DNA_sequence
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    @main_vbox = vbox
+    create_buttons
+    create_left_buffer  # Our left buffer.
+    create_right_buffer # Our right buffer.
+    create_top_hbox     # This should come after the two buffers.
+    create_middle_bar_containing_the_arrow_pointing_to_the_right_side
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
+  end
+
+  # ========================================================================= #
+  # === top_hbox?
+  # ========================================================================= #
+  def top_hbox?
+    @dataset[:top_hbox]
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+    @main_vbox.maximal(top_hbox?, 4)
+    @main_vbox.maximal(@middle_bar)
+    button_box = button_box(
+      @dataset[:backtrack_button],
+      @dataset[:quit_button]
+    )
+    button_box.vertical_layout
+    @main_vbox.minimal(button_box)
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << @main_vbox
+    ::UniversalWidgets.set_main_window(window)
+    upon_delete_event_quit_the_application
+    window.use_this_font = font?
+    window.show_all
+    window.set_size_request(width?, height?)
+    window.set_default_size(width?, height?)
+    window.set_padding(padding?)
+    window.set_border_size(border_size?)
+    window.top_left
+    run_main
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::AminoacidComposition[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::AminoacidComposition.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::ProteinToDNA.new(i)
+    )
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::AminoacidComposition.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::AminoacidComposition.start_gui_application
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::UniversalWidgets::AminoacidComposition.new(ARGV)
+end # gtkproteintodna