Class: Bioroebe::GUI::UniversalWidgets::RandomSequence

Inherits:
UniversalWidgets::Base
  • Object
show all
Includes:
CommandlineArguments, Bioroebe::GUI
Defined in:
lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb

Overview

Bioroebe::GUI::UniversalWidgets::RandomSequence

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
'Random Sequence - for DNA, RNA and aminoacids'
WIDTH =
#

WIDTH

#
'75% or 1200px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 980px minimum'
FONT_LARGE =
#

FONT_LARGE

#
'Calibri 32'
MONOSPACED_FONT =
#

MONOSPACED_FONT

When this font is changed, don’t forget to also change the font at SMALLER_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_HEADER =
#

USE_THIS_HEADER

#
['one-letter abbreviation', 'n times']
GENERATE_N_AMINOACIDS_BY_DEFAULT =
#

GENERATE_N_AMINOACIDS_BY_DEFAULT

#
15

Constants included from Bioroebe::GUI

ARRAY_ALL_GTK_WIDGETS, FONT_SIZE, OLD_VERBOSE_VALUE, Bioroebe::GUI::USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Bioroebe::GUI

#disable_warnings, #enable_warnings, #log_dir?

Methods included from CommandlineArguments

#commandline_arguments?, #commandline_arguments_that_are_files?, #e, #first?, #first_non_hyphen_argument?, #remove_hyphens_from_the_commandline_arguments, #return_commandline_arguments_as_string, #return_commandline_arguments_that_are_not_files, #return_entries_without_two_leading_hyphens, #select_commandline_arguments, #select_entries_starting_with_two_hyphens, #set_commandline_arguments

Methods included from ColoursForBase

#colourize_this_aminoacid_sequence_for_the_commandline, #colourize_this_nucleotide_sequence, #disable_colours, #ecomment, #efancy, #egold, #enable_colours, #eorange, #eparse, #erev, #red, #remove_trailing_escape_part, #return_colour_for_nucleotides, #rev, #sdir, #set_will_we_use_colours, #sfancy, #sfile, #simp, #swarn, #use_colours?, #use_colours_within_the_bioroebe_namespace?

Constructor Details

#initialize(commandline_arguments = nil, run_already = true) ⇒ RandomSequence

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 91

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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::GUI::UniversalWidgets::RandomSequence[]

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 609

def self.[](i = ARGV)
  new(i)
end

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::RandomSequence.run

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 616

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::RandomSequence.new(i)
  )
  r.background_colour(:white)
  return r
end

Instance Method Details

#aminoacid_sequence? ⇒ Boolean Also known as: sequence?, main_sequence?

#

aminoacid_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 523

def aminoacid_sequence?
  @entry_containing_the_sequence.text?.to_s
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 136

def border_size?
  4
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 576

def connect_the_skeleton
  abort_on_exception

  vbox1 = create_vbox
  vbox1.minimal(@top_bar,                                      3)
  vbox1.minimal(@entry_containing_the_sequence,                3)
  vbox1.minimal(@button_for_generating_a_new_random_sequence,  3)
  vbox1.minimal(@entry_for_n_entries_in_the_sequence,          3)
  hbox_for_the_button_copy_to_clipboard = create_hbox
  hbox_for_the_button_copy_to_clipboard.minimal(@button_copy_to_clipboard)
  hbox_for_the_button_copy_to_clipboard.align_into_the_center
  vbox1.minimal(hbox_for_the_button_copy_to_clipboard,         3)
  vbox1.minimal(@statistical_widget_top_panel,                 0)
  vbox1.maximal(@statistical_widget,                           3)

  window = runner_widget(nil, width?, height?, title?)
  window << vbox1

  ::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

#create_statistical_information ⇒ Object

#

create_statistical_information

This method will fill up the “table”.

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 465

def create_statistical_information
  create_statistical_top_panel
  @statistical_widget = create_vbox
  # ======================================================================= #
  # Next we must create the widget that can hold the hash. This will
  # be a list-store that can be dynamically updated.
  # ======================================================================= #
  array1 = ::Bioroebe.return_array_of_common_aminoacids
  array2 = Array.new(array1.size, '0')
  array = array1.zip(array2) # Zip it up with 0-values here.
  array.prepend(USE_THIS_HEADER)
  # ======================================================================= #
  # Next the tree view is created:
  # ======================================================================= #
  @tree_view, @list_store = tree_widget_with_two_columns_per_row(array)
  do_properly_setup_the_tree_view
  scrolled_window = create_scrolled_window(@tree_view)
  scrolled_window.set_border_width(10)
  scrolled_window.bblack1
  @statistical_widget.maximal(scrolled_window, 5)
  hbox1 = create_hbox
  hbox1.minimal(@clear_button)
  hbox1.align_into_the_center
  @statistical_widget.minimal(hbox1, 2)
  enable_proper_sorting_for_the_list_store
  on_right_click_in_the_tree_view_deselect_the_selection
end

#create_statistical_top_panel ⇒ Object

#

create_statistical_top_panel

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 283

def create_statistical_top_panel
  # ======================================================================= #
  # This here has to be added separately from the scrolled-window.
  # ======================================================================= #
  @statistical_widget_top_panel = bold_label(
    'Showing statistical information about the '\
    'assigned aminoacid sequence next'
  )
end

#create_the_buttons ⇒ Object

#

create_the_buttons (buttons tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 248

def create_the_buttons
  # ======================================================================= #
  # === @clear_button
  # ======================================================================= #
  @clear_button = bold_button('_Clear the table above', self, :use_mnemonics) {
    :do_clear_the_list_store
  }
  @clear_button.hint = 'Clear the above dataset / table'
  @clear_button.set_name('button1')
  # ======================================================================= #
  # === @button_for_generating_a_new_random_sequence
  # ======================================================================= #
  @button_for_generating_a_new_random_sequence = bold_button(
    '_Generate a random aminoacid sequence',
    self,
    :use_mnemonics
  ) {{ # Add a tooltip.
    tooltip: 'Clicking on this button will <b>generate a random '\
             'aminoacid sequence</b>. Do not set a too high value '\
             'as that may take a long time, and consume a '\
             'lot of memory/RAM.'
  }}
  @button_for_generating_a_new_random_sequence.on_click_event {
    do_generate_a_random_sequence(n_aminoacids?)
  }
  @button_for_generating_a_new_random_sequence.set_name('button1')
  # ======================================================================= #
  # Next, create, then add the clipboard button:
  # ======================================================================= #
  create_the_copy_to_clipboard_button
end

#create_the_copy_to_clipboard_button ⇒ Object

#

create_the_copy_to_clipboard_button

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 168

def create_the_copy_to_clipboard_button
  # ======================================================================= #
  # === @button_copy_to_clipboard
  # ======================================================================= #
  @button_copy_to_clipboard = bold_button('_Copy to the xorg-clipboard',
    self, :use_mnemonic) {
    :do_copy_to_the_clipboard
  }
  @button_copy_to_clipboard.hint = 'This will <b>copy the aminoacid '\
    'sequence</b> to the <b>xorg-clipboard</b>.'
  @button_copy_to_clipboard.set_name('button1')
end

#create_the_entries ⇒ Object

#

create_the_entries

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 435

def create_the_entries
  # ======================================================================= #
  # === @entry_containing_the_sequence
  # ======================================================================= #
  @entry_containing_the_sequence = create_entry
  @entry_containing_the_sequence.on_click_select_everything
  @entry_containing_the_sequence.yellow_background
  @entry_containing_the_sequence.bblack1
  # ======================================================================= #
  # Add the entry that allows the user to control how many aminoacids
  # will be "generated".
  # ======================================================================= #
  @entry_for_n_entries_in_the_sequence = create_entry { :align_center }
  @entry_for_n_entries_in_the_sequence.set_text(GENERATE_N_AMINOACIDS_BY_DEFAULT.to_s)
  @entry_for_n_entries_in_the_sequence.yellow_background
  @entry_for_n_entries_in_the_sequence.on_click_select_everything
  @entry_for_n_entries_in_the_sequence.bblack1
  @entry_for_n_entries_in_the_sequence.on_enter {
    do_generate_a_random_sequence_using_the_value_from_the_proper_entry
  }
  @entry_for_n_entries_in_the_sequence.hint = 'Input here how many random '\
    'amino acids should be generated.'
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 238

def create_the_skeleton
  create_the_buttons # Call this before the top_bar is created.
  create_statistical_information # Call this before the top-bar is created.
  create_the_top_bar
  create_the_entries
end

#create_the_top_bar ⇒ Object

#

create_the_top_bar

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 317

def create_the_top_bar
  @top_bar = gtk_top_bar
  button_open_file = button('_Open File', self, :use_mnemonics) {
    :do_open_a_file_and_then_set_the_correct_values
  }
  button_open_file.hint = 'Click on this button to open a local FASTA '\
                          'file.'
  button_open_file.bblack1
  @top_bar.add(button_open_file)
  # ======================================================================= #
  # === @combo_box_for_the_sequence_type
  # ======================================================================= #
  @combo_box_for_the_sequence_type = combo_box_entry(
    %w( aminoacid DNA RNA )
  )
  @combo_box_for_the_sequence_type.first_is_active
  # ======================================================================= #
  # Respond to the event when the combo-box value changes:
  # ======================================================================= #
  @combo_box_for_the_sequence_type.on_changed {
    _ = @combo_box_for_the_sequence_type.text?
    @button_for_generating_a_new_random_sequence.set_text(
      "Generate a random #{_} sequence"
    )
    @button_for_generating_a_new_random_sequence.make_bold
    @statistical_widget_top_panel.set_text(
      "Showing statistical information about the "\
      "assigned #{_} sequence next"
    )
    @statistical_widget_top_panel.make_bold
    @tree_view.model = nil
    @list_store = nil
    @list_store = gtk_list_store(String, String)
    case mode?
    when 'DNA','RNA'
      if mode? == 'DNA'
        array1 = %w( A T C G )
      else
        array1 = %w( A U C G )
      end
      array2 = Array.new(array1.size, '0')
      zipped = array1.zip(array2) # Zip it up with 0-values here.
      zipped.each {|a, b|
        iter = @list_store.append
        iter.set_value(0, a)
        iter.set_value(1, b)
      }
    else # else we assume a protein.
    end
    @tree_view.model = @list_store
  }
  @top_bar.add(@combo_box_for_the_sequence_type)
end

#do_clear_the_list_store ⇒ Object

#

do_clear_the_list_store

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 296

def do_clear_the_list_store
  @list_store.clear
end

#do_copy_to_the_clipboard ⇒ Object

#

do_copy_to_the_clipboard

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 414

def do_copy_to_the_clipboard
  begin
    require 'xorg_buffer'
  rescue LoadError; end
  if Object.const_defined? :XorgBuffer
    XorgBuffer.copy_this_text_to_the_clipboard(aminoacid_sequence?)
  else
    e 'The gem xorg_buffer is not installed, or could not be found.'
  end
end

#do_evaluate_the_sequence(use_this_sequence = main_sequence? ) ⇒ Object

#

do_evaluate_the_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 374

def do_evaluate_the_sequence(
    use_this_sequence = main_sequence?
  )
  do_clear_the_list_store
  case mode?
  # ======================================================================= #
  # === DNA
  # ======================================================================= #
  when 'DNA','RNA'
    @tree_view.remove_the_columns
    column1 = ::Gtk::TreeViewColumn.new('DNA-Nucleotide', gtk_cell_renderer_text, { text: 0 })
    column2 = ::Gtk::TreeViewColumn.new('n times',        gtk_cell_renderer_text, { text: 1 })
    # ======================================================================= #
    # Add the two columns to the tree-view next.
    # ======================================================================= #
    @tree_view.append_column(column1)
    @tree_view.append_column(column2)
    @tree_view.is_sortable
    if mode? == 'DNA'
      array1 = %w( A T C G )
    else
      array1 = %w( A U C G )
    end
    array2 = Array.new(array1.size, '0')
    array2 = Bioroebe.return_DNA_composition_hash(use_this_sequence).values.map(&:to_s)
    array = array1.zip(array2)
  # ======================================================================= #
  # === aminoacids
  # ======================================================================= #
  when 'aminoacids'
    array1 = ::Bioroebe.return_array_of_common_aminoacids
    array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_sequence).values.map(&:to_s)
    array = array1.zip(array2) # Zip it up with 0-values here.
  end
  ::Gtk.populate_this_liststore(@list_store, array)
end

#do_generate_a_random_sequence(n_aminoacids = :default) ⇒ Object

#

do_generate_a_random_sequence

This is the method that will be run whenever a new random aminoacid sequence is to be generated.

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 187

def do_generate_a_random_sequence(
    n_aminoacids = :default
  )
  case n_aminoacids
  when nil, :default
    n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
  end
  n_aminoacids = n_aminoacids.to_s
  # ======================================================================= #
  # We also must update the entry that displays the aminoacids. We have
  # to check whether we use aminoacids or not, though.
  # ======================================================================= #
  case mode?
  when /RNA/i,
       /DNA/i
    use_this_as_the_new_sequence = :: Bioroebe.generate_random_dna_sequence(n_aminoacids).to_s
    array1 = Bioroebe::DNA_NUCLEOTIDES
    if mode?.to_s == 'RNA'
      use_this_as_the_new_sequence = ::Bioroebe.generate_random_rna_sequence(n_aminoacids).to_s
      array1 = Bioroebe::RNA_NUCLEOTIDES
    end
    hash = {}
    array1.each {|this_key|
      hash[this_key] = 0
    }
    use_this_as_the_new_sequence.chars.each {|this_nucleotide|
      hash[this_nucleotide.to_s] += 1
    }
    array2 = hash.values.map {|entry| entry.to_s }
  else # else assume protein sequence
    use_this_as_the_new_sequence = ::Bioroebe.create_random_aminoacids(n_aminoacids).to_s
    array1 = ::Bioroebe.return_array_of_common_aminoacids
    array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_as_the_new_sequence).values.map(&:to_s)
  end
  @entry_containing_the_sequence.set_content(use_this_as_the_new_sequence)
  # ======================================================================= #
  # Next we have to build up our array, which is then passed into the
  # list-store.
  # ======================================================================= #
  array = array1.zip(array2) # Zip it up with 0-values here.
  # ======================================================================= #
  # Next, populate the liststore with the new data - since as of July
  # 2022 we will sort it based on most aminoacids though:
  # ======================================================================= #
  array = array.sort_by {|a, b| b }.reverse # This sorts by highest first.
  ::Gtk.populate_this_liststore(@list_store, array)
end

#do_generate_a_random_sequence_using_the_value_from_the_proper_entry(i = n_aminoacids? ) ⇒ Object

#

do_generate_a_random_sequence_using_the_value_from_the_proper_entry

This variant will be guaranteed to use the value determined by the gtk entry.

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 507

def do_generate_a_random_sequence_using_the_value_from_the_proper_entry(
    i = n_aminoacids?
  )
  do_generate_a_random_sequence(i)
end

#do_open_a_file_and_then_set_the_correct_values ⇒ Object

#

do_open_a_file_and_then_set_the_correct_values

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 531

def do_open_a_file_and_then_set_the_correct_values
  filename = ::Gtk.select_file(self) {{ # @parent_widget should be of Gtk::Window class or subclass.
    show_hidden:                true,
    add_these_shortcut_folders: ::Bioroebe.log_dir?,
    current_folder:             ::Bioroebe.log_dir?
  }}
  if File.exist? filename
    _ = filename
    if _.end_with? '.fasta'
      require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
      sequence = Bioroebe.parse_fasta_file(_).sequence?
      set_main_input(sequence)
      do_evaluate_the_sequence
    else
      set_main_input(File.read(_).strip)
    end
  end
end

#do_properly_setup_the_tree_view ⇒ Object

#

do_properly_setup_the_tree_view

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 496

def do_properly_setup_the_tree_view
  @tree_view.linear_sorting
  @tree_view.the_headers_can_be_dragged
end

#enable_proper_sorting_for_the_list_store ⇒ Object

#

enable_proper_sorting_for_the_list_store

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 553

def enable_proper_sorting_for_the_list_store
  # ======================================================================= #
  # Sort the number-of-entries found entry a bit differently. This
  # will sort by putting the most frequently occurring aminoacids
  # or DNA/RNA nucleotides on top.
  # ======================================================================= #
  @list_store.set_sort_func(1) { |_model, iter1, iter2|
    iter2[1].to_i <=> iter1[1].to_i
  }
end

#handle_CSS_rules ⇒ Object Also known as: handle_CSS

#

handle_CSS_rules (CSS tag, css tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 157

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
'
  apply_the_CSS_rules
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 143

def main_font?
  USE_THIS_FONT
end

#mode? ⇒ Boolean

#

mode?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 310

def mode?
  @combo_box_for_the_sequence_type.text?
end

#n_aminoacids? ⇒ Boolean

#

n_aminoacids?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 428

def n_aminoacids?
  @entry_for_n_entries_in_the_sequence.text?.to_s
end

#on_right_click_in_the_tree_view_deselect_the_selection ⇒ Object

#

on_right_click_in_the_tree_view_deselect_the_selection

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 567

def on_right_click_in_the_tree_view_deselect_the_selection
  @tree_view.on_right_mouse_button_clicked {|widget, event|
    @tree_view.deselect_everything
  }
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 129

def padding?
  8
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 106

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?
  # ======================================================================= #
  # === @list_store
  # ======================================================================= #
  @list_store = nil
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 516

def run
  run_super
end

#set_main_input(i) ⇒ Object

#

set_main_input

#


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 303

def set_main_input(i)
  @entry_containing_the_sequence.set_text(i.to_s)
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/random_sequence/random_sequence.rb', line 150

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end