Class: Bioroebe::GUI::UniversalWidgets::ShowCodonTable

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

Overview

Bioroebe::GUI::UniversalWidgets::ShowCodonTable

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
'Show Codon Table'
WIDTH =
#

WIDTH

#
'75% or 2000px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 500px 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_20
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
HEADER_TO_USE_FOR_THE_TREE_VIEW =
#

HEADER_TO_USE_FOR_THE_TREE_VIEW

#
[
  'Local Path',
  'File size',
  'n nucleotides',
  '%GC'
]

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) ⇒ ShowCodonTable

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 88

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::ShowCodonTable[]

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 789

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::ShowCodonTable.run

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 796

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

Instance Method Details

#A ⇒ Object

#

A

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 318

def A
  label('A')
end

#active_text? ⇒ Boolean Also known as: selected?

#

active_text?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 311

def active_text?
  @combo_box_containing_the_registered_codon_tables.selected?.to_s
end

#attach_all_proper_values_to_the_main_table ⇒ Object

#

attach_all_proper_values_to_the_main_table

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 138

def attach_all_proper_values_to_the_main_table
                               # left_attach, right_attach, top_attach, bottom_attach. 
  @table.attach_defaults(label(''), 0,1, 0, 1)
  @table.attach_defaults(bold_T(), 1,2, 0, 1)
  @table.attach_defaults(C().set_name('bold_royalblue'), 2,3, 0, 1)
  @table.attach_defaults(A().set_name('bold_royalblue'), 3,4, 0, 1)
  @table.attach_defaults(G().set_name('bold_royalblue'), 4,5, 0, 1)
  @table.attach_defaults(label(''), 5,6, 0, 1)

  # ======================================================================= #
  # === T
  # ======================================================================= #
  @table.attach_defaults(bold_T(), 0,1, 1, 2)
  @table.attach_defaults(@table_hash['TTT'] = label('    '), 1,2, 1, 2)
  @table.attach_defaults(@table_hash['TCT'] = label('    '), 2,3, 1, 2)
  @table.attach_defaults(@table_hash['TAT'] = label('    '), 3,4, 1, 2)
  @table.attach_defaults(@table_hash['TGT'] = label('    '), 4,5, 1, 2)
  @table.attach_defaults(bold_T(),5,6, 1, 2)

  # ======================================================================= #
  # === T
  # ======================================================================= #
  @table.attach_defaults(bold_T(), 0,1, 2, 3)
  @table.attach_defaults(@table_hash['TTC'] = label, 1,2, 2, 3)
  @table.attach_defaults(@table_hash['TCC'] = label, 2,3, 2, 3)
  @table.attach_defaults(@table_hash['TAC'] = label, 3,4, 2, 3)
  @table.attach_defaults(@table_hash['TGC'] = label, 4,5, 2, 3)
  @table.attach_defaults(bold_C(),5,6, 2, 3)

  # ======================================================================= #
  # === T
  # ======================================================================= #
  @table.attach_defaults(bold_T(), 0,1, 3, 4)
  @table.attach_defaults(@table_hash['TTA'] = label, 1,2, 3, 4)
  @table.attach_defaults(@table_hash['TCA'] = label, 2,3, 3, 4)
  @table.attach_defaults(@table_hash['TAA'] = label, 3,4, 3, 4)
  @table.attach_defaults(@table_hash['TGA'] = label, 4,5, 3, 4)
  @table.attach_defaults(bold_A(), 5,6, 3, 4)

  # ======================================================================= #
  # === T
  # ======================================================================= #
  @table.attach_defaults(bold_T(), 0,1, 4, 5)
  @table.attach_defaults(@table_hash['TTG'] = label, 1,2, 4, 5)
  @table.attach_defaults(@table_hash['TCG'] = label, 2,3, 4, 5)
  @table.attach_defaults(@table_hash['TAG'] = label, 3,4, 4, 5)
  @table.attach_defaults(@table_hash['TGG'] = label,4,5, 4, 5)
  @table.attach_defaults(bold_G(), 5,6, 4, 5)

  # ======================================================================= #
  # === C
  # ======================================================================= #
  @table.attach_defaults(bold_C(), 0,1, 5, 6)
  @table.attach_defaults(@table_hash['CTT'] = label, 1,2, 5, 6)
  @table.attach_defaults(@table_hash['CCT'] = label, 2,3, 5, 6)
  @table.attach_defaults(@table_hash['CAT'] = label, 3,4, 5, 6)
  @table.attach_defaults(@table_hash['CGT'] = label,4,5, 5, 6)
  @table.attach_defaults(bold_T(), 5,6, 5, 6)

  # ======================================================================= #
  # === C
  # ======================================================================= #
  @table.attach_defaults(bold_C(), 0,1, 6, 7)
  @table.attach_defaults(@table_hash['CTC'] = label, 1,2, 6, 7)
  @table.attach_defaults(@table_hash['CCC'] = label, 2,3, 6, 7)
  @table.attach_defaults(@table_hash['CAC'] = label, 3,4, 6, 7)
  @table.attach_defaults(@table_hash['CGC'] = label, 4,5, 6, 7)
  @table.attach_defaults(bold_C(), 5,6, 6, 7)

  # ======================================================================= #
  # === C
  # ======================================================================= #
  @table.attach_defaults(bold_C(), 0,1, 7, 8)
  @table.attach_defaults(@table_hash['CTA'] = label, 1,2, 7, 8)
  @table.attach_defaults(@table_hash['CCA'] = label, 2,3, 7, 8)
  @table.attach_defaults(@table_hash['CAA'] = label, 3,4, 7, 8)
  @table.attach_defaults(@table_hash['CGA'] = label, 4,5, 7, 8)
  @table.attach_defaults(bold_A(), 5,6, 7, 8)

  # ======================================================================= #
  # === C
  # ======================================================================= #
  @table.attach_defaults(bold_C(), 0,1, 8, 9)
  @table.attach_defaults(@table_hash['CTG'] = label, 1,2, 8, 9)
  @table.attach_defaults(@table_hash['CCG'] = label, 2,3, 8, 9)
  @table.attach_defaults(@table_hash['CAG'] = label, 3,4, 8, 9)
  @table.attach_defaults(@table_hash['CGG'] = label,4,5, 8, 9)
  @table.attach_defaults(bold_G(), 5,6, 8, 9)

  # ======================================================================= #
  # === A
  # ======================================================================= #
  @table.attach_defaults(bold_A(), 0,1, 9, 10)
  @table.attach_defaults(@table_hash['ATT'] = label, 1,2, 9, 10)
  @table.attach_defaults(@table_hash['ACT'] = label, 2,3, 9, 10)
  @table.attach_defaults(@table_hash['AAT'] = label, 3,4, 9, 10)
  @table.attach_defaults(@table_hash['AGT'] = label, 4,5, 9, 10)
  @table.attach_defaults(bold_T(), 5,6, 9, 10)

  # ======================================================================= #
  # === A
  # ======================================================================= #
  @table.attach_defaults(bold_A(), 0,1, 10, 11)
  @table.attach_defaults(@table_hash['ATC'] = label, 1,2, 10, 11)
  @table.attach_defaults(@table_hash['ACC'] = label, 2,3, 10, 11)
  @table.attach_defaults(@table_hash['AAC'] = label, 3,4, 10, 11)
  @table.attach_defaults(@table_hash['AGC'] = label, 4,5, 10, 11)
  @table.attach_defaults(bold_C(), 5,6, 10, 11)

  # ======================================================================= #
  # === A
  # ======================================================================= #
  @table.attach_defaults(bold_A(), 0,1, 11, 12)
  @table.attach_defaults(@table_hash['ATA'] = label, 1,2, 11, 12)
  @table.attach_defaults(@table_hash['ACA'] = label, 2,3, 11, 12)
  @table.attach_defaults(@table_hash['AAA'] = label, 3,4, 11, 12)
  @table.attach_defaults(@table_hash['AGA'] = label, 4,5, 11, 12)
  @table.attach_defaults(bold_A(), 5,6, 11, 12)

  # ======================================================================= #
  # === A
  # ======================================================================= #
  @table.attach_defaults(bold_A(), 0,1, 12, 13)
  @table.attach_defaults(@table_hash['ATG'] = label, 1,2, 12, 13)
  @table.attach_defaults(@table_hash['ACG'] = label, 2,3, 12, 13)
  @table.attach_defaults(@table_hash['AAG'] = label, 3,4, 12, 13)
  @table.attach_defaults(@table_hash['AGG'] = label,4,5, 12, 13)
  @table.attach_defaults(bold_G(), 5,6, 12, 13)

  # ======================================================================= #
  # === G
  # ======================================================================= #
  @table.attach_defaults(bold_G(), 0,1, 13, 14)
  @table.attach_defaults(@table_hash['GTT'] = label, 1,2, 13, 14)
  @table.attach_defaults(@table_hash['GCT'] = label, 2,3, 13, 14)
  @table.attach_defaults(@table_hash['GAT'] = label, 3,4, 13, 14)
  @table.attach_defaults(@table_hash['GGT'] = label, 4,5, 13, 14)
  @table.attach_defaults(bold_T(), 5,6, 13, 14)

  # ======================================================================= #
  # === G
  # ======================================================================= #
  @table.attach_defaults(bold_G(), 0,1, 14, 15)
  @table.attach_defaults(@table_hash['GTC'] = label, 1,2, 14, 15)
  @table.attach_defaults(@table_hash['GCC'] = label, 2,3, 14, 15)
  @table.attach_defaults(@table_hash['GAC'] = label, 3,4, 14, 15)
  @table.attach_defaults(@table_hash['GGC'] = label,4,5, 14, 15)
  @table.attach_defaults(bold_C(), 5,6, 14, 15)

  # ======================================================================= #
  # === G
  # ======================================================================= #
  @table.attach_defaults(bold_G(), 0,1, 15, 16)
  @table.attach_defaults(@table_hash['GTA'] = label, 1,2, 15, 16)
  @table.attach_defaults(@table_hash['GCA'] = label, 2,3, 15, 16)
  @table.attach_defaults(@table_hash['GAA'] = label, 3,4, 15, 16)
  @table.attach_defaults(@table_hash['GGA'] = label,4,5, 15, 16)
  @table.attach_defaults(bold_A(), 5,6, 15, 16)

  # ======================================================================= #
  # === G
  # ======================================================================= #
  @table.attach_defaults(bold_G(), 0,1, 16, 17)
  @table.attach_defaults(@table_hash['GTG'] = label, 1,2, 16, 17)
  @table.attach_defaults(@table_hash['GCG'] = label, 2,3, 16, 17)
  @table.attach_defaults(@table_hash['GAG'] = label, 3,4, 16, 17)
  @table.attach_defaults(@table_hash['GGG'] = label, 4,5, 16, 17)
  @table.attach_defaults(bold_G(), 5,6, 16, 17)
end

#bold_A ⇒ Object

#

bold_A

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 346

def bold_A
  _ = A().set_name('bold_royalblue')
  _.make_selectable
  return _
end

#bold_C ⇒ Object

#

bold_C

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 364

def bold_C
  _ = C().set_name('bold_royalblue')
  _.make_selectable
  return _
end

#bold_G ⇒ Object

#

bold_G

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 373

def bold_G
  _ = G().set_name('bold_royalblue')
  _.make_selectable
  return _
end

#bold_T ⇒ Object

#

bold_T

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 355

def bold_T
  _ = T().set_name('bold_royalblue')
  _.make_selectable
  return _
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 405

def border_size?
  2
end

#C ⇒ Object

#

C

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 325

def C
  label('C')
end

#change_label(i) ⇒ Object

#

change_label

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 492

def change_label(i)
  case i.label.to_s
  when 'A'
    i.set_text('C')
  when 'C'
    i.set_text('T')
  when 'T'
    i.set_text('G')
  when 'G'
    i.set_text('A')
  end
  i.make_bold
  determine_the_codon_for_the_last_button
end

#clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table ⇒ Object

#

clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 622

def clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table
  _ = active_text?.split(' ').first.to_s
  if _ and !_.empty?
    new_dataset = @all_codon_tables[_]
    @main_hash.clear
    @main_hash.merge!(new_dataset)
    sync_the_dataset_onto_the_main_table
  end
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 751

def connect_the_skeleton
  abort_on_exception

  # ======================================================================= #
  # The left vbox will contain the scrolled-window.
  # ======================================================================= #
  left_vbox = create_vbox
  left_vbox.minimal(@scrolled_window)
  right_vbox = create_vbox
  right_vbox.minimal(@label_and_combo_box,                         2)
  right_vbox.minimal(gtk_horizontal_spacer,                        2)
  right_vbox.minimal(return_widget_containing_the_toggle_buttons, 12)
  _ = drag_it_left_to_right(left_vbox, right_vbox)
  _.position = width? / 4.5
  main_box = can_be_dragged_up_and_down(
    top_box?,
    _
  )

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

  ::UniversalWidgets.set_main_window(window)
  upon_delete_event_quit_the_application
  clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table
  window.use_this_font = font?
  window.show_all
  window.set_padding(padding?)
  window.set_border_size(border_size?)
  window.set_size_request(width?, height?)
  window.set_default_size(width?, height?)
  window.top_left
  run_main
end

#create_the_box_containing_the_label_and_the_combobox ⇒ Object

#

create_the_box_containing_the_label_and_the_combobox

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 635

def create_the_box_containing_the_label_and_the_combobox
  # ======================================================================= #
  # === @label_and_combo_box
  # ======================================================================= #
  @label_and_combo_box = create_vbox
  @label_and_combo_box.minimal(
    left_aligned_label(
      ' Select the codon table (default: <b>eukaryotes</b>)'
    ), 8
  )
  @label_and_combo_box.make_selectable
  hbox = create_hbox
  hbox.minimal(@combo_box_containing_the_registered_codon_tables, 2)
  @label_and_combo_box.minimal(
    hbox, 2
  )
end

#create_the_combo_box_containing_the_available_codon_tables ⇒ Object Also known as: create_the_combo_box

#

create_the_combo_box_containing_the_available_codon_tables

This method will create the main combo-box.

#


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

def create_the_combo_box_containing_the_available_codon_tables
  @combo_box_containing_the_registered_codon_tables = combo_box_text
  @combo_box_containing_the_registered_codon_tables.bblack1
  @combo_box_containing_the_registered_codon_tables.pad4px
  do_populate_the_combo_box
  @combo_box_containing_the_registered_codon_tables.first_entry_is_active
  # ======================================================================= #
  # React to the combo-box's value changing - must come after the
  # combo box was populated with data:
  # ======================================================================= #
  @combo_box_containing_the_registered_codon_tables.on_changed {
    clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table
    update_the_main_header
  }
end

#create_the_main_table ⇒ Object

#

create_the_main_table (table tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 474

def create_the_main_table
  @table = create_table(8, 20, true)
  @table.set_name('table_bblack1')
  @table.set_column_spacings(5) # And a decent column spacing as well.
  @table.set_row_spacings(1)    # Also use a decent row-spacing.
  @table.set_border_width(12)   # Make the "border" noticable.
end

#create_the_scrolled_window_then_add_the_table_into_it ⇒ Object

#

create_the_scrolled_window_then_add_the_table_into_it

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 524

def create_the_scrolled_window_then_add_the_table_into_it
  # ======================================================================= #
  # === @scrolled_window
  # ======================================================================= #
  @scrolled_window = create_scrolled_window(@table) { :automatic }
  @scrolled_window.bblack1
  @scrolled_window.pad6px
  @scrolled_window.set_size_request(240, 780)
  @scrolled_window.use_this_font = smaller_font?
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 724

def create_the_skeleton
  create_the_title_bar
  create_the_combo_box_containing_the_available_codon_tables
  create_the_box_containing_the_label_and_the_combobox
  create_the_top_vbox # Must come after create_the_title_bar().
  create_the_main_table
  attach_all_proper_values_to_the_main_table
  create_the_scrolled_window_then_add_the_table_into_it
end

#create_the_title_bar ⇒ Object

#

create_the_title_bar

This is the “title” bar, the main header, on top of the widget.

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 456

def create_the_title_bar
  hbox = create_hbox
  # ======================================================================= #
  # For the following gtk-label, always keep a leading ' '.
  # ======================================================================= #
  @label_for_the_title_bar = label(
    ' Standard (Eukaryote) Codon Table (codon table number: 1)'
  )
  @label_for_the_title_bar.left_align
  @label_for_the_title_bar.set_name('h1')
  hbox.minimal(image_starred,            4)
  hbox.minimal(@label_for_the_title_bar, 4)
  @title_bar = hbox
end

#create_the_top_vbox ⇒ Object

#

create_the_top_vbox

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 570

def create_the_top_vbox
  @top_vbox = create_vbox
  @top_vbox.add(horizontal_spacer)
  @top_vbox.add(@title_bar)
  @top_vbox.add(horizontal_spacer)
end

#determine_the_codon_for_the_last_button ⇒ Object

#

determine_the_codon_for_the_last_button

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 510

def determine_the_codon_for_the_last_button
  first  = @button1.text?.to_s
  second = @button2.text?.to_s
  third  = @button3.text?.to_s
  codon = first+second+third
  if @main_hash.has_key? codon
    @button4.set_text(@main_hash[codon])
    @button4.make_bold
  end
end

#do_populate_the_combo_box ⇒ Object

#

do_populate_the_combo_box

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 382

def do_populate_the_combo_box
  # ======================================================================= #
  # Populate the combo-box with our dataset.
  # ======================================================================= #
  array = []
  hash = ::Bioroebe.hash_codon_tables?
  hash.each_pair {|key, value|
    value = uniform_length(value) 
    array << "#{key} (#{value})"
  }
  @combo_box_containing_the_registered_codon_tables.populate_with(array)
end

#G ⇒ Object

#

G

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 339

def G
  label('G')
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/show_codon_table/show_codon_table.rb', line 707

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
tooltip {
padding:      25px;
border-width: 3px;
border-style: dotted;
border-color: orange;
}
'
  apply_the_CSS_rules
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 556

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 398

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 103

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?
  # ======================================================================= #
  # === @main_hash
  #
  # This is the hash that will store the new dataset.
  # ======================================================================= #
  @main_hash = {}
  # ======================================================================= #
  # === @table_hash
  # ======================================================================= #
  @table_hash = {}
  # ======================================================================= #
  # === @all_codon_tables
  #
  # Use a "pointer" towards all codon tables.
  # ======================================================================= #
  @all_codon_tables = return_all_codon_tables
end

#return_all_codon_tables ⇒ Object

#

return_all_codon_tables

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 549

def return_all_codon_tables
  ::Bioroebe.codon_tables
end

#return_widget_containing_the_toggle_buttons ⇒ Object

#

return_widget_containing_the_toggle_buttons

These are the four “toggle” buttons on the right side of the widget.

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 658

def return_widget_containing_the_toggle_buttons
  hbox = create_hbox
  hbox.pad8px
  @button1 = bold_button('T')
  @button1.foreground_colour = :royalblue
  @button1.bblack1
  @button1.on_clicked {
    change_label(@button1)
  }
  @button2 = create_bold_button('T')
  @button2.foreground_colour = :royalblue
  @button2.bblack1
  @button2.on_clicked {
    change_label(@button2)
  }
  @button3 = create_bold_button('T')
  @button3.foreground_colour = :royalblue
  @button3.bblack1
  @button3.on_clicked {
    change_label(@button3)
  }
  # ======================================================================= #
  # Next comes the button that will also show '*'.
  # ======================================================================= #
  @button4 = create_bold_button('T')
  @button4.foreground_colour = :crimson
  @button4.bblack1
  @button4.set_name('custom_tooltip')
  @button4.hint =
    "\nThis button is special in that it will denote "\
    "the current aminoacid. The other three buttons "\
    "represent the codon at different positions.\n\n"\
    "A '<b>*</b>' indicates a stop-codon.\n"
  # button4.on_clicked {
  #   change_label(button4)
  # }
  bbox = gtk_button_box_spread(
    @button1,
    @button2,
    @button3
  )
  hbox.minimal(bbox,                             2)
  hbox.minimal(gtk_button_box_spread(@button4), 10)
  return hbox
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 737

def run
  run_super
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 563

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#smaller_font? ⇒ Boolean

#

smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 744

def smaller_font?
  SMALLER_FONT
end

#sync_this_dataset_onto_the_main_table(i = @main_hash) ⇒ Object Also known as: sync_the_dataset_onto_the_main_table

#

sync_this_dataset_onto_the_main_table

Note that this method not only syncs the dataset, as such, but it will also change some CSS rules as-is, in particular to enable different colours (red or forestgreen or black). This is made possible thanks to the support via .set_name().

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 585

def sync_this_dataset_onto_the_main_table(
    i = @main_hash
  )
  i.each_pair {|key, value|
    widget = @table_hash[key]
    if widget
      value = value.to_s
      # =================================================================== #
      # Handle key and value separately next:
      # =================================================================== #
      case value
      when '*' # Rewrite '*' to 'STOP'.
        value = 'STOP'
        widget.set_name('red')
      else
        widget.set_name('black')
      end
      case key
      when i['START']
        widget.set_text("#{value}*")
        widget.set_name('forestgreen')
      else
        # ================================================================= #
        # .center(4) is necessary because, oddly enough, two codon tables
        # have no stop codons - or the dataset is wrong. Either way it
        # makes sense to use 4 here; see the string "STOP" too which
        # has four characters.
        # ================================================================= #
        widget.set_text(value.center(4))
      end
    end
  }
end

#T ⇒ Object

#

T

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 332

def T
  label('T')
end

#top_box? ⇒ Boolean

#

top_box?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 485

def top_box?
  @top_vbox
end

#uniform_length(i) ⇒ Object

#

uniform_length

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 538

def uniform_length(i)
  i = i.dup
  if i.size > 45
    i[45 ..-1] = '[...]'
  end
  return i
end

#update_the_main_header ⇒ Object

#

update_the_main_header

This method will update the main header (which is on top of the widget).

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_table/show_codon_table.rb', line 436

def update_the_main_header
  _ = active_text?
  codon_table_number = 0
  if _.include? '('
    codon_table_number = _.split('(').first.to_s.strip
    _ = _.scan(/\((.+)\)/).flatten.first
  end
  _ = _.dup
  if _.size > 45 # Shrink it a bit in this case.
    _ = _[0 .. 45]+' [...]'
  end
  _ << ' Codon Table (codon table number: '+codon_table_number.to_s+')'
  @label_for_the_title_bar.set_text(_)
end