bioroebe 0.12.24 → 0.13.31

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

@@ -0,0 +1,665 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::UniversalWidgets::AntiSenseStrand
+#
+# This widget contains two entries (user input fields). These two entries
+# correspond to sense and anti-sense in a DNA strand.
+#
+# In the first entry the user may only enter "atcg". These will be
+# UPCASED automatically, so the real input will be "ATCG",
+# respectively.
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::AntiSenseStrand.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/universal_widgets/hamming_distance/hamming_distance.rb'
+# =========================================================================== #
+require 'universal_widgets/base/base.rb'
+
+module Bioroebe
+
+module GUI
+
+module UniversalWidgets
+
+class AntiSenseStrand < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::AntiSenseStrand
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
+
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  #
+  # Specify which title to use for this small widget.
+  # ========================================================================= #
+  TITLE = 'Sense / Anti-Sense Strand'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '65% or 500px minimum'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '55% or 300px minimum'
+
+  # ========================================================================= #
+  # === TEXT_COMPARE_THE_TWO_SEQUENCES
+  # ========================================================================= #
+  TEXT_COMPARE_THE_TWO_SEQUENCES = '_Compare the two sequences'
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === MAX_LENGTH
+  # ========================================================================= #
+  MAX_LENGTH = 50_000
+
+  # ========================================================================= #
+  # === IMG_DNA_HELIX
+  # ========================================================================= #
+  IMG_DNA_HELIX =
+    '/home/x/data/images/science/biology/DNA_HELIX.jpg'
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === 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'
+
+  # ========================================================================= #
+  # === PADDING_TO_USE
+  # ========================================================================= #
+  PADDING_TO_USE = 12
+
+  # ========================================================================= #
+  # === DEFAULT_TEXT_FOR_ENTRY1
+  # ========================================================================= #
+  DEFAULT_TEXT_FOR_ENTRY1 = 'AGUUCGAUGGAAAATAT'
+
+  # ========================================================================= #
+  # === DEFAULT_TEXT_FOR_ENTRY2
+  # ========================================================================= #
+  DEFAULT_TEXT_FOR_ENTRY2 = 'AGUCCGGUCGAAAAAAA'
+
+  # ========================================================================= #
+  # === 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_border_width(5)
+  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
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    PADDING_TO_USE
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    8
+  end
+
+  # ========================================================================= #
+  # === seq1?
+  # ========================================================================= #
+  def seq1?
+    @entry_on_top.text
+  end
+
+  # ========================================================================= #
+  # === seq2?
+  # ========================================================================= #
+  def seq2?
+    @entry_on_bottom.text
+  end
+
+  # ========================================================================= #
+  # === entry1?
+  # ========================================================================= #
+  def entry1?
+    @entry_on_top
+  end; alias entry1 entry1? # === entry1
+
+  # ========================================================================= #
+  # === create_the_entries                           (entries tag, entry tag)
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # === @entry_n_differences
+    #
+    # This is the entry that will simply show the number of differences
+    # between the two sequences, as a number.
+    # ======================================================================= #
+    @entry_n_differences = entry_with_icon_name('edit-undo-symbolic-rtl.symbolic')
+    @entry_n_differences.xalign = 0.5 # Align towards the center.
+    @entry_n_differences.bblack1
+    @entry_n_differences.clear_background
+    @entry_n_differences.yellow_background
+
+    # ======================================================================= #
+    # === @entry_on_top
+    # ======================================================================= #
+    @entry_on_top = create_entry(DEFAULT_TEXT_FOR_ENTRY1)
+    @entry_on_top.set_font(MONOSPACED_FONT)
+    @entry_on_top.clear_background
+    @entry_on_top.css_class('BG_lightsteelblue')
+    @entry_on_top.bblack1
+    @entry_on_top.on_changed { do_calculate_the_differences }
+    @entry_on_top.hint = 'This entry should contain the first sequence (seq1).'
+    @entry_on_top.set_max_length(50_000)
+    @entry_on_top.on_key_press_event { |widget, event|
+      old_text = widget.text
+      keyname = Gdk::Keyval.to_name(event.keyval)
+      case keyname.upcase
+      when *%w( A T C G U )
+        # This is ok.
+      when *%w( B D E F H I J K L M N O P Q R S V W X Y Z ) # Otherwise set the old input here.
+        unless event.state.control_mask? # This snippet checks whether a key-combination has been used.
+          widget.set_text(old_text.upcase)
+        end
+      end
+    } if false # disabled as of August 2022.
+    # ======================================================================= #
+    # And keep things upcased here:
+    # ======================================================================= #
+    @entry_on_top.on_key_release { |widget, event|
+      old_text = @entry_on_top.text
+      new_text = @entry_on_top.text.upcase
+      unless old_text == new_text
+        @entry_on_top.set_text(new_text)
+        @entry_on_top.move_cursor_to_the_most_right_position
+      end
+    }
+
+    # ======================================================================= #
+    # === @entry_on_bottom
+    # ======================================================================= #
+    @entry_on_bottom = create_entry(DEFAULT_TEXT_FOR_ENTRY2)
+    @entry_on_bottom.set_font(MONOSPACED_FONT)
+    @entry_on_bottom.css_classes('clear_background BG_lightsteelblue')
+    @entry_on_bottom.bblack1
+    @entry_on_bottom.on_changed { do_calculate_the_differences }
+    @entry_on_bottom.hint = 'This entry should contain the second sequence (seq2).'
+    @entry_on_bottom.set_max_length(50_000)
+  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
+
+  # ========================================================================= #
+  # === 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_compare_button
+  #
+  # This method will create the button that will compare the two sequences.
+  # ========================================================================= #
+  def create_compare_button
+    # ======================================================================= #
+    # === @compare_button
+    # ======================================================================= #
+    @compare_button = bold_button(TEXT_COMPARE_THE_TWO_SEQUENCES, self, :use_mnemonics) {
+      :consider_sanitizing_the_input_and_then_compare_the_two_sequences
+    }
+    @compare_button.apply_markup
+    @compare_button.on_hover(:lightblue)
+    @compare_button.set_name('button1')
+    @compare_button.hint = 'Click this button to '\
+      '<span weight="bold" foreground="lightblue">compare</span> '\
+      'the two sequences.'
+  end
+
+  # ========================================================================= #
+  # === consider_sanitizing_the_input_and_then_compare_the_two_sequences
+  # ========================================================================= #
+  def consider_sanitizing_the_input_and_then_compare_the_two_sequences
+    consider_sanitizing_the_input
+    compare_the_two_sequences
+  end
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    create_the_entries
+    # ======================================================================= #
+    # === The top box
+    # ======================================================================= #
+    @top_box = vbox
+
+    @label_on_top = bold_label(TITLE)
+    @label_on_top.hint = 
+      "Only <b>valid nucleotides</b> (A, T, C, G, U) \n"\
+      "can be accepted as input."
+    # ======================================================================= #
+    # Create the top hbox for string1 next:
+    # ======================================================================= #
+    @hbox_for_string1 = create_hbox
+    @hbox_for_string1.minimal(text('1').make_bold, 1)
+    @hbox_for_string1.maximal(@entry_on_top, 1)
+
+    # ======================================================================= #
+    # Create the bottom hbox for string2 next:
+    # ======================================================================= #
+    @hbox_for_string2 = create_hbox
+    @hbox_for_string2.minimal(text('2').make_bold, 1)
+    @hbox_for_string2.maximal(@entry_on_bottom, 1)
+
+    create_compare_button
+
+    small_hbox = create_hbox
+    # ======================================================================= #
+    # === n_differences found Gtk::Text
+    # ======================================================================= #
+    short_text_widget = text('<b>n differences</b> found:')
+    short_text_widget.do_markify
+    small_hbox.minimal(short_text_widget, 2)
+    small_hbox.hint =
+      'This entry will show <b>how many differences</b> '\
+      'exist between these two strings.'
+    small_hbox.minimal(@entry_n_differences, 2)
+    # ======================================================================= #
+    # === The bottom box
+    # ======================================================================= #
+    @bottom_box = create_vbox
+    @bottom_box.pack_start(@compare_button, expand: false, fill: false, padding: 1)
+    @bottom_box.pack_start(small_hbox, expand: false, fill: true, padding: 0)
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
+  end
+
+  # ========================================================================= #
+  # === top_hbox?
+  # ========================================================================= #
+  def top_hbox?
+    @dataset[:top_hbox]
+  end
+
+  # ========================================================================= #
+  # === do_upcase_all_entries
+  # ========================================================================= #
+  def do_upcase_all_entries
+    [
+      @entry_on_top,
+      @entry_on_bottom
+    ].each {|entry|
+      entry.do_upcase
+    }
+  end
+
+  # ========================================================================= #
+  # === consider_sanitizing_the_input
+  # ========================================================================= #
+  def consider_sanitizing_the_input
+    # ======================================================================= #
+    # The following two lines were added as of 07.05.2020.
+    # ======================================================================= #
+    @entry_on_top.set_text(@entry_on_top.text.delete('-'))
+    @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
+    do_upcase_all_entries
+  end
+
+  # ========================================================================= #
+  # === synchronize_anti_sense
+  #
+  # Will fetch content and synchronize the @entry_anti_sense
+  # ========================================================================= #
+  def synchronize_anti_sense
+    this_text = ''.dup
+    @entry_sense.text?.each_char { |char|
+      case char
+      when 'A' then this_text << 'T'
+      when 'T' then this_text << 'A'
+      when 'C' then this_text << 'G'
+      when 'G' then this_text << 'C'
+      end
+    }
+    @entry_anti_sense.set_text(this_text)
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+
+    # ======================================================================= #
+    # @top_box is an instance of gtk-vbox.
+    # ======================================================================= #
+    @top_box.minimal(@label_on_top,     1)
+    text = left_aligned_text(
+        "The <b>Hamming distance</b> - a number - measures the number of "\
+        "\npositions at which two strings of equal length are "\
+        "different.")
+    text.make_selectable
+    text.use_this_font = SMALLER_FONT
+    @top_box.minimal(text,              12)
+    @top_box.minimal(@hbox_for_string1,  2)
+    @top_box.minimal(@hbox_for_string2,  2)
+
+    vpaned = mouse_draggable_via_up_and_down_movement(@top_box, @bottom_box)
+    vpaned.set_size_request(width?, 550)
+
+    Thread.new {
+      sleep 0.01
+      @entry_n_differences.do_focus
+      entry1?.deselect
+      do_compare
+    }
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << vpaned
+    ::UniversalWidgets.set_main_window(window)
+    upon_delete_event_quit_the_application
+    jump_into_the_first_entry
+    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
+
+  # ========================================================================= #
+  # === jump_into_the_first_entry
+  # ========================================================================= #
+  def jump_into_the_first_entry
+    entry1?.do_focus
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::AntiSenseStrand[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::AntiSenseStrand.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    r = ::Gtk.runner_factory(
+      ::Bioroebe::GUI::Gtk::AntiSenseStrand.new(i)
+    )
+    r.modify_background(:normal, :mintcream)
+    return r
+  end; self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::AntiSenseStrand.run_gtk3_widget
+       self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::AntiSenseStrand.start_gui_application
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::UniversalWidgets::AntiSenseStrand.new(ARGV)
+end # gtkproteintodna