Class: Bioroebe::GUI::Gtk::ShowCodonTable

Inherits:
Gtk::Box
  • Object
show all
Includes:
ShowCodonTableModule, Gtk::BaseModule
Defined in:
lib/bioroebe/gui/gtk3/show_codon_table/misc.rb,
lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb

Overview

Bioroebe::GUI::Gtk::ShowCodonTable

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
USE_THIS_FONT =
#

USE_THIS_FONT

We need a mono-spaced font here; Source Code Pro seems fine.

#
:hack_18

Constants included from ShowCodonTableModule

ShowCodonTableModule::HEIGHT, ShowCodonTableModule::TITLE, ShowCodonTableModule::WIDTH

Class Method Summary collapse

Instance Method Summary collapse

Methods included from ShowCodonTableModule

#active_text?, #padding?, #reset_the_shared_module

Constructor Details

#initialize(commandline_arguments = ARGV, run_already = true) ⇒ ShowCodonTable

#

initialize

#

31
32
33
34
35
36
37
38
39
40
41
42
43
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 31

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  super(:vertical)
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  signal_destroy_then_quit
  set_title(TITLE) if respond_to?(:set_title)
  run if run_already
end

Class Method Details

.run(i = ARGV) ⇒ Object

#

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

#

390
391
392
393
394
395
396
397
398
399
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 390

def self.run(
    i = ARGV
  )
  require 'gtk_paradise/run'
  _ = ::Bioroebe::GUI::Gtk::ShowCodonTable.new(i)
  r = ::Gtk.run
  r << _
  r.automatic_size_then_automatic_title
  r.top_left_then_run
end

Instance Method Details

#A ⇒ Object

#

A

#

239
240
241
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 239

def A
  label('A')
end

#attach_all_proper_values_to_the_main_table ⇒ Object

#

attach_all_proper_values_to_the_main_table

#

66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
145
146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
212
213
214
215
216
217
218
219
220
221
222
223
224
225
226
227
228
229
230
231
232
233
234
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 66

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

#

267
268
269
270
271
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 267

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

#bold_C ⇒ Object

#

bold_C

#

285
286
287
288
289
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 285

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

#bold_G ⇒ Object

#

bold_G

#

294
295
296
297
298
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 294

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

#bold_T ⇒ Object

#

bold_T

#

276
277
278
279
280
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 276

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

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

337
338
339
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 337

def border_size?
  2
end

#C ⇒ Object

#

C

#

246
247
248
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 246

def C
  label('C')
end

#change_label(i) ⇒ Object

#

change_label

#

344
345
346
347
348
349
350
351
352
353
354
355
356
357
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 344

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

#

546
547
548
549
550
551
552
553
554
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 546

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_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
140
141
142
143
144
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 125

def connect_skeleton
  abort_on_exception
  # ======================================================================= #
  # The left vbox will contain the scrolled-window.
  # ======================================================================= #
  left_vbox = gtk_vbox
  left_vbox.minimal(@scrolled_window)
  right_vbox = gtk_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?,
    _
  )
  minimal(main_box)
  show_all
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#

149
150
151
152
153
154
155
156
157
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 149

def create_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_box_containing_the_label_and_the_combobox ⇒ Object

#

create_the_box_containing_the_label_and_the_combobox

#

95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 95

def create_the_box_containing_the_label_and_the_combobox
  # ======================================================================= #
  # === @label_and_combo_box
  # ======================================================================= #
  @label_and_combo_box = gtk_vbox
  @label_and_combo_box.minimal(
    left_aligned_label(
      ' Select the codon table (default: <b>eukaryotes</b>)'
    ), 8
  )
  hbox = gtk_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.

#

406
407
408
409
410
411
412
413
414
415
416
417
418
419
420
421
422
423
424
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 406

def create_the_combo_box_containing_the_available_codon_tables
  if use_gtk2?
    @combo_box_containing_the_registered_codon_tables = gtk_combo_box
  else
    @combo_box_containing_the_registered_codon_tables = gtk_combo_box_text
  end
  @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)

#

470
471
472
473
474
475
476
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 470

def create_the_main_table
  @table = gtk_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

#

376
377
378
379
380
381
382
383
384
385
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 376

def create_the_scrolled_window_then_add_the_table_into_it
  # ======================================================================= #
  # === @scrolled_window
  # ======================================================================= #
  @scrolled_window = gtk_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_title_bar ⇒ Object

#

create_the_title_bar

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

#

452
453
454
455
456
457
458
459
460
461
462
463
464
465
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 452

def create_the_title_bar
  hbox = gtk_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

#

115
116
117
118
119
120
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 115

def create_the_top_vbox
  @top_vbox = gtk_vbox
  @top_vbox.add(gtk_horizontal_spacer)
  @top_vbox.add(@title_bar)
  @top_vbox.add(gtk_horizontal_spacer)
end

#determine_the_codon_for_the_last_button ⇒ Object

#

determine_the_codon_for_the_last_button

#

362
363
364
365
366
367
368
369
370
371
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 362

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

#

303
304
305
306
307
308
309
310
311
312
313
314
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 303

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

#

260
261
262
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 260

def G
  label('G')
end

#handle_CSS ⇒ Object

#

handle_CSS

#

537
538
539
540
541
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 537

def handle_CSS
  use_gtk_paradise_project_css_file
  use_project_css_file
  apply_the_CSS
end

#reset ⇒ Object

#

reset (reset tag)

#

35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 35

def reset
  reset_the_internal_variables
  reset_the_shared_module
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, NAMESPACE]
  set_use_this_font(USE_THIS_FONT)
  handle_CSS
  infer_the_size_automatically
  # ======================================================================= #
  # === @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

#

330
331
332
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 330

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.

#

50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 50

def return_widget_containing_the_toggle_buttons
  hbox = gtk_hbox
  hbox.pad8px
  @button1 = gtk_bold_button('T')
  @button1.foreground_colour = :royalblue
  @button1.bblack1
  @button1.on_clicked {
    change_label(@button1)
  }
  @button2 = gtk_bold_button('T')
  @button2.foreground_colour = :royalblue
  @button2.bblack1
  @button2.on_clicked {
    change_label(@button2)
  }
  @button3 = gtk_bold_button('T')
  @button3.foreground_colour = :royalblue
  @button3.bblack1
  @button3.on_clicked {
    change_label(@button3)
  }
  @button4 = gtk_bold_button('T')
  @button4.foreground_colour = :crimson
  @button4.bblack1
  @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 '*' 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)

#

162
163
164
165
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb', line 162

def run
  create_skeleton_then_connect_skeleton
  clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table
end

#smaller_font? ⇒ Boolean

#

smaller_font?

#

Returns:

  • (Boolean) 

488
489
490
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 488

def smaller_font?
  :hack_16
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().

#

500
501
502
503
504
505
506
507
508
509
510
511
512
513
514
515
516
517
518
519
520
521
522
523
524
525
526
527
528
529
530
531
532
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 500

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

#

253
254
255
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 253

def T
  label('T')
end

#top_box? ⇒ Boolean

#

top_box?

#

Returns:

  • (Boolean) 

481
482
483
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 481

def top_box?
  @top_vbox
end

#uniform_length(i) ⇒ Object

#

uniform_length

#

319
320
321
322
323
324
325
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 319

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).

#

432
433
434
435
436
437
438
439
440
441
442
443
444
445
 
# File 'lib/bioroebe/gui/gtk3/show_codon_table/misc.rb', line 432

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