Class: Bioroebe::GUI::Gtk::FormatConverter

Inherits:
Gtk::Box
  • Object
show all
Includes:
Gtk::BaseModule
Defined in:
lib/bioroebe/gui/gtk3/format_converter/format_converter.rb

Overview

Bioroebe::GUI::Gtk::FormatConverter

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
'Format Converter'
WIDTH =
#

WIDTH

#
'60% or 800px minimum'
HEIGHT =
#

HEIGHT

#
800
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_20

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

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

#

initialize

#


53
54
55
56
57
58
59
60
61
62
63
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 53

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  super(:vertical)
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  run if run_already
end

Class Method Details

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::FormatConverter.run

#


331
332
333
334
335
336
337
338
339
340
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 331

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

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


90
91
92
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 90

def border_size?
  0
end

#calculated_weight?(i) ⇒ Boolean

#

calculated_weight?

#

Returns:

  • (Boolean) 


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

def calculated_weight?(i)
  this_file = Bioroebe.file_molecular_weight
  dataset = YAML.load_file(this_file)
  weight = 0
  if i.is_a?(String) and !i.empty?
    chars = i.chars.sort
    chars.each {|this_char|
      value = dataset[this_char]
      weight += value if value
    }
  end
  # ======================================================================= #
  # Must deduct water too.
  # ======================================================================= #
  weight -= (18.0 * (i.size - 1))
  return weight.round(2)
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#


248
249
250
251
252
253
254
255
256
257
258
259
260
261
262
263
264
265
266
267
268
269
270
271
272
273
274
275
276
277
278
279
280
281
282
283
284
285
286
287
288
289
290
291
292
293
294
295
296
297
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 248

def connect_skeleton
  abort_on_exception
  _ = gtk_left_aligned_label('Format Converter')
  _.make_bold
  minimal(_, 2)
  if first?
    @entry_input_sequence.set_text(first?.to_s)
  end
  hbox = gtk_hbox
  hbox.maximal(@entry_input_sequence, 1)
  event_box = gtk_event_box(image_file_open)
  event_box.hint = 'Click on this button in order to '\
    'open a local .FASTA file.'
  event_box.on_clicked {
    do_open_a_local_file
  }
  hbox.minimal(event_box,       1)
  add(hbox)
  @entry_input_sequence.on_enter {
    simulate_enter_click
  }
  hbox = gtk_hbox
  # ======================================================================= #
  # === button_do_convert
  # ======================================================================= #
  button_do_convert = gtk_button('_Do convert')
  button_do_convert.remove_background
  button_do_convert.bblack1
  button_do_convert.pad6px
  button_do_convert.on_clicked {
    do_convert_the_file
  }
  hbox.minimal(button_do_convert, 4)
  @combo_box = gtk_combo_box(
    %w( to_fasta )
  )
  @combo_box.bblack1
  @combo_box.first_is_active
  hbox.minimal(@combo_box, 4)
  minimal(hbox, 10)
  scrolled_window = gtk_scrolled_window(@text_view) { :always }
  scrolled_window.width_height(300, 600)
  scrolled_window.bblack1
  scrolled_window.css_class('pad2px')
  minimal(scrolled_window, 2)
  @label_n_aminoacids = left_aligned_text
  minimal(@label_n_aminoacids, 2)
  @label_molecular_weight = left_aligned_text
  minimal(@label_molecular_weight, 2)
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#


216
217
218
219
220
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 216

def create_skeleton
  @text_buffer = gtk_text_buffer
  @text_view   = gtk_text_view(@text_buffer)
  create_user_input
end

#create_user_input ⇒ Object

#

create_user_input

#


97
98
99
100
101
102
103
104
105
106
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 97

def create_user_input
  # ======================================================================= #
  # === @entry_input_sequence
  # ======================================================================= #
  @entry_input_sequence = gtk_entry
  @entry_input_sequence.hint = 'This will denote the current file.'
  @entry_input_sequence.bblack1
  @entry_input_sequence.yellow_background
  @entry_input_sequence.pad5px
end

#do_convert_the_file ⇒ Object

#

do_convert_the_file

#


189
190
191
192
193
194
195
196
197
198
199
200
201
202
203
204
205
206
207
208
209
210
211
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 189

def do_convert_the_file
  _ = main_entry?.text?
  if _.empty?
    popup_over_this_widget(
      main_entry?,
      ' Please assign a file to work with first. '
    )
  else
    text = @combo_box.text?
pp text
pp text
pp text
pp _
pp _
pp _
    case text
    when 'to_fasta'
pp File.read(_)
      result = Bioroebe.genbank_to_fasta(File.read(_))
pp result
    end
  end
end

#do_open_a_local_file(this_widget = @parent_widget) ⇒ Object

#

do_open_a_local_file

#


302
303
304
305
306
307
308
309
310
311
312
313
314
315
316
317
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 302

def do_open_a_local_file(
    this_widget = @parent_widget
  )
  require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
  widget = ::Gtk::SelectFile.new(this_widget) {{
    current_folder:         ::Bioroebe.log_dir?,
    additional_directories: ::Bioroebe.log_dir?
  }}
  this_file = widget.do_pick_file.text.to_s
  if File.exist?(this_file) and File.file?(this_file) # Ensure that it really is a file.
    dataset = File.read(this_file)
    set_main_entry(this_file.to_s)
    fill_with_this(dataset.to_s)
  end
  return this_file
end

#fill_with_this(i) ⇒ Object

#

fill_with_this

#


118
119
120
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 118

def fill_with_this(i)
  @text_buffer.set_text(i)
end

#main_entry? ⇒ Boolean

#

main_entry?

#

Returns:

  • (Boolean) 


181
182
183
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 181

def main_entry?
  @entry_input_sequence
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#


225
226
227
228
229
230
231
232
233
234
235
236
237
238
239
240
241
242
243
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 225

def menu(
    i = commandline_arguments?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i
    # ===================================================================== #
    # === gtk_aminoacid_composition --ubi
    # ===================================================================== #
    when /^-?-?ubiquitin$/i,
         /^-?-?ubi$/i
      set_main_entry(
        Bioroebe.return_ubiquitin_sequence
      )
      simulate_enter_click
    end
  end
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


83
84
85
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 83

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#


68
69
70
71
72
73
74
75
76
77
78
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 68

def reset
  reset_the_internal_variables
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, NAMESPACE]
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
  use_gtk_paradise_project_css_file
  append_project_CSS_file 
  infer_the_size_automatically
end

#run ⇒ Object

#

run (run tag)

#


322
323
324
325
326
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 322

def run
   ::Bioroebe.cd(::Bioroebe.log_dir?) 
  create_skeleton_then_connect_skeleton
  menu
end

#set_main_entry(i) ⇒ Object Also known as: set_main_input_sequence

#

set_main_entry

#


167
168
169
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 167

def set_main_entry(i)
  @entry_input_sequence.set_text(i.to_s)
end

#set_main_input_sequence_and_evaluate_it(i) ⇒ Object

#

set_main_input_sequence_and_evaluate_it

#


174
175
176
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 174

def set_main_input_sequence_and_evaluate_it(i)
  simulate_enter_click(i)
end

#set_parent_widget(i) ⇒ Object

#

set_parent_widget

#


111
112
113
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 111

def set_parent_widget(i)
  @parent_widget = i
end

#simulate_enter_click(_ = @entry_input_sequence.text?) ⇒ Object

#

simulate_enter_click

#


146
147
148
149
150
151
152
153
154
155
156
157
158
159
160
161
162
 
# File 'lib/bioroebe/gui/gtk3/format_converter/format_converter.rb', line 146

def simulate_enter_click(
    _ = @entry_input_sequence.text?
  )
  _.upcase!
  _ = ::Bioroebe.filter_away_invalid_aminoacids(_)
  @entry_input_sequence.set_text(_)
  fill_the_table_data_with_this_sequence(_)
  @label_n_aminoacids.set_text(
    "This sequence has <b>#{_.size}</b> aminoacids."
  )
  @label_n_aminoacids.do_markify
  @label_molecular_weight.set_text(
    'The molecular weight is: <b>'+
    calculated_weight?(_).to_s+'</b> Dalton'
  )
  @label_molecular_weight.do_markify
end