Class: Bioroebe::GUI::Gtk::DnaToAminoacidWidget

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

Overview

Bioroebe::GUI::Gtk::DnaToAminoacidWidget

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
'DNA to Aminoacid Sequence converter'
WIDTH =
#

WIDTH

#
'80%'
HEIGHT =
#

HEIGHT

#
'35% or minimum 120px'
MAIN_FONT =
#

MAIN_FONT

#
:dejavu_condensed_16
SMALLER_FONT =
#

SMALLER_FONT

#
:dejavu_condensed_14

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

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

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 64

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

Class Method Details

.[](i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::DnaToAminoacidWidget[]

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 613

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 620

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

Instance Method Details

#assign_this_fasta_file(i) ⇒ Object

#

assign_this_fasta_file

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 499

def assign_this_fasta_file(i)
  i = ::Bioroebe.parse_fasta(i).sequence?
  i.upcase! if i
  set_dna_sequence(i)
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 126

def border_size?
  4
end

#button_trigger_the_conversion? ⇒ Boolean

#

button_trigger_the_conversion?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 211

def button_trigger_the_conversion?
  @button_trigger_conversion
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 313

def connect_skeleton
  abort_on_exception
  # ======================================================================= #
  # The two top labels denote which widget is the one for the DNA
  # sequence, and which one is for the aminoacid sequence.
  # ======================================================================= #
  dna_sequence_label       = bold_label('DNA sequence')
  dna_sequence_label.set_size_request(sanitized_half_width, 42)
  aminoacid_sequence_label = bold_label('Aminoacid sequence')
  aminoacid_sequence_label.set_size_request(sanitized_half_width, 42)
  # ======================================================================= #
  # API for .attach() is:
  #   .attach(child, left, top, width, height)
  # ======================================================================= #
  @grid.attach(dna_sequence_label,                    0, 0, 2, 1)
  @grid.attach(aminoacid_sequence_label,              3, 0, 2, 1)
  @grid.attach(@left_entry,                           0, 1, 2, 1)
  @grid.attach(@event_box_containing_the_right_arrow, 2, 1, 1, 1)
  @grid.attach(@right_entry,                          3, 1, 2, 1)
  button_box = simplified_button_box(button_trigger_the_conversion?)
  button_box.set_size_request(350, 40)
  @grid.attach(
    button_box, 0, 2, 5, 1
  )
  minimal(@header_bar)
  add(horizontal_spacer)
  minimal(@grid, 8)
  add(horizontal_spacer)
  hbox = gtk_hbox
  # ======================================================================= #
  # Add the dropdown box next; also known as the combobox.
  # ======================================================================= #
  dropdown_box = gtk_dropdown_box(
    Bioroebe.available_codon_tables?
  )
  dropdown_box.use_this_font = SMALLER_FONT
  dropdown_box.first_element_is_active
  dropdown_box.bblack1
  dropdown_box.pad5px
  dropdown_box.hint = 'When a new codon table is assigned, via the '\
    'drop-down menu, then any assigned DNA sequence will be automatically '\
    'translated to its corresponding amino acid sequence.'
  dropdown_box.on_changed {
    new_text = dropdown_box.text?.to_s
    @entry_for_the_codon_table_in_use.set_text(new_text)
    do_determine_the_aminoacid_sequence
  }
  hbox.minimal(text('Codon table in use:'),       3)
  hbox.minimal(@entry_for_the_codon_table_in_use, 3)
  hbox.minimal(dropdown_box,                      3)
  add(hbox)
  vbox = gtk_vbox
  # ======================================================================= #
  # === @label_n_DNA_nucleotides
  # ======================================================================= #
  @label_n_DNA_nucleotides = bold_label('n DNA nucleotides: ')
  @label_n_DNA_nucleotides.align_left
  @label_n_DNA_nucleotides.make_selectable
  vbox.add(@label_n_DNA_nucleotides)
  @label_n_aminoacids = bold_label('n aminoacids:      ')
  @label_n_aminoacids.align_left
  @label_n_aminoacids.make_selectable
  vbox.add(@label_n_aminoacids)
  minimal(vbox)
end

#create_button_trigger_conversion ⇒ Object

#

create_button_trigger_conversion

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 576

def create_button_trigger_conversion
  # ======================================================================= #
  # === @button_trigger_conversion
  # ======================================================================= #
  @button_trigger_conversion = bold_button('_Trigger Conversion')
  @button_trigger_conversion.clear_background
  @button_trigger_conversion.disallow_resizing
  @button_trigger_conversion.set_size_request(125, 40)
  @button_trigger_conversion.set_background_colour :whitesmoke
  @button_trigger_conversion.on_hover(:lightgreen)
  @button_trigger_conversion.on_clicked {
    update_the_dna_sequence_then_do_the_conversion
    do_properly_space_the_top_left_entry
  }
  @button_trigger_conversion.bblack2
  # ======================================================================= #
  # Use a tooltip as well for our button:
  # ======================================================================= #
  @button_trigger_conversion.hint = 
    "Clicking on this button will convert from a <b>DNA</b> "\
    "<b>sequence</b> \n(on the left hand side) to the <b>corresponding "\
    "Aminoacid sequence</b>.\n\nMake sure you input the DNA sequence "\
    "on the left hand side. The space character, aka ' ', will "\
    "be ignored."
end

#create_grid ⇒ Object

#

create_grid (grid tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 225

def create_grid
  # ======================================================================= #
  # === @grid
  # ======================================================================= #
  @grid = gtk_grid
  @grid.set_column_spacing(5)
  @grid.set_row_spacing(5)
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 565

def create_skeleton
  create_the_header_bar
  create_grid
  create_button_trigger_conversion
  create_the_entries
  create_the_event_box
end

#create_the_entries ⇒ Object

#

create_the_entries (entries tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 174

def create_the_entries
  create_the_left_entry
  create_the_right_entry
  create_the_entry_for_the_codon_table_in_use
end

#create_the_entry_for_the_codon_table_in_use ⇒ Object

#

create_the_entry_for_the_codon_table_in_use

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 183

def create_the_entry_for_the_codon_table_in_use
  # ======================================================================= #
  # === @entry_for_the_codon_table_in_use
  # ======================================================================= #
  @entry_for_the_codon_table_in_use = gtk_entry(Bioroebe.codon_table_in_use?.to_s)
  @entry_for_the_codon_table_in_use.center
  @entry_for_the_codon_table_in_use.bblack2
  @entry_for_the_codon_table_in_use.bg_azure
  @entry_for_the_codon_table_in_use.read_only
  @entry_for_the_codon_table_in_use.use_this_font = SMALLER_FONT
  @entry_for_the_codon_table_in_use.width_height(450, 42)
end

#create_the_event_box ⇒ Object

#

create_the_event_box

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 199

def create_the_event_box
  @event_box_containing_the_right_arrow = gtk_eventbox(
    gtk_label(:arrow_right)
  )
  @event_box_containing_the_right_arrow.on_clicked {
    update_the_dna_sequence_then_do_the_conversion
  }
end

#create_the_header_bar ⇒ Object

#

create_the_header_bar

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 382

def create_the_header_bar
  @header_bar = return_default_header_bar
  @header_bar.pad8px
  @header_bar.bblack1
  button_open_file = icon_theme(:open_file)
  button_open_file.hint = 'Click on this button to open a '\
                          'local FASTA file.'
  button_open_file.on_clicked {
    result = do_pick_a_local_file
    if result and File.file?(result) and result.end_with?('.fasta','.fa')
      assign_this_fasta_file(result)
    end
  }
  @header_bar.pack_left(button_open_file)
end

#create_the_left_entry ⇒ Object

#

create_the_left_entry (left tag)

This entry will keep the DNA sequence.

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 479

def create_the_left_entry
  # ======================================================================= #
  # The left entry, a DNA widget as a gtk-entry widget.
  # ======================================================================= #
  @left_entry = gtk_entry
  @left_entry.clear_background
  @left_entry.yellow_background
  @left_entry.bblack1
  @left_entry.pad5px
  @left_entry.set_size_request(sanitized_half_width, 42)
  @left_entry.hint = 'You can either hit the enter key here, or '\
    'click the trigger-conversion button.'
  @left_entry.on_enter_key {
    update_the_dna_sequence_then_do_the_conversion
  }
end

#create_the_right_entry ⇒ Object

#

create_the_right_entry

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 293

def create_the_right_entry
  # ======================================================================= #
  # === The right Aminoacid widget.
  # ======================================================================= #
  @right_entry = gtk_entry
  @right_entry.clear_background
  @right_entry.lightskyblue_background
  @right_entry.bblack1
  @right_entry.pad5px
  @right_entry.set_size_request(sanitized_half_width, 42)
  # ======================================================================= #
  # The AA widget. Will be highlighted on a click event. This was
  # reconsidered and disabled as of August 2021.
  # ======================================================================= #
  # @right_entry.on_click_event { :select_text }
end

#dna_sequence? ⇒ Boolean Also known as: return_the_main_DNA_sequence

#

dna_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 167

def dna_sequence?
  left_entry?.text.to_s
end

#do_pick_a_local_file ⇒ Object

#

do_pick_a_local_file (open tag)

This method is run when the user wants to open a local file.

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 403

def do_pick_a_local_file
  create_a_new_file_chooser_dialog(self) {{
    start_dir:              return_pwd,
    show_hidden_files:      :yes,
    current_folder:         ::Bioroebe.log_dir?,
    additional_directories: [
      ::Bioroebe.log_dir?,
      ENV['PC'].to_s,
      ENV['MY_TEMP'].to_s,
      ENV['RSRC'].to_s
    ]
  }}
  _ = ::Gtk.main_file?.to_s
  return _
end

#do_properly_space_the_top_left_entry ⇒ Object

#

do_properly_space_the_top_left_entry

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 251

def do_properly_space_the_top_left_entry
  old_text = @left_entry.text?.delete(' ')
  _ = old_text.
      gsub(/(.{3})/,' \1').
      lstrip
  @left_entry.set_text(_)
end

#do_the_conversion(i = @dna_sequence) ⇒ Object Also known as: do_sync_fields, do_trigger_the_conversion, do_determine_the_aminoacid_sequence

#

do_the_conversion (conversion tag)

This is the method that is to be used for the actual conversion.

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 517

def do_the_conversion(
    i = @dna_sequence
  )
  # ======================================================================= #
  # Next, we must translate from DNA to Aminoacid sequence.
  # ======================================================================= #
  sanitized_input = i.delete(' ').delete('-')
  i.tr!('U','T') if i.include? 'U'
  set_dna_sequence(i)
  if ::Bioroebe.const_defined? :Controller
    # ===================================================================== #
    # Ok, in this case we can store the dataset via a class-method.
    # ===================================================================== #
    ::Bioroebe::GUI::Controller.set_dna_sequence(i)
  end
  aminoacid_sequence = ::Bioroebe.convert_dna_to_protein_sequence(
    sanitized_input,
    :default,
    Bioroebe::CodonTable.by_name(
      entry_for_the_codon_table?.text?
    )
  )
  set_aminoacid_sequence(aminoacid_sequence)
  update_the_entries
  sync_the_entries_back_onto_the_two_main_strings
  if @parent_widget and @parent_widget.respond_to?(:set_aminoacid_sequence)
    @parent_widget.set_aminoacid_sequence(aminoacid_sequence)
  end
  @label_n_DNA_nucleotides.set_text(
    'n DNA nucleotides: '+
    i.delete(' ').
      delete('-').size.to_s
  )
  @label_n_DNA_nucleotides.make_bold
  @label_n_DNA_nucleotides.align_left
  @label_n_aminoacids.set_text(
    'n aminoacids:      '+
    aminoacid_sequence.size.to_s
  )
  @label_n_aminoacids.make_bold
  @label_n_aminoacids.align_left
end

#entry_for_the_codon_table? ⇒ Boolean

#

entry_for_the_codon_table?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 262

def entry_for_the_codon_table?
  @entry_for_the_codon_table_in_use
end

#handle_CSS_rules ⇒ Object

#

handle_CSS_rules

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 111

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_CSS_file 
end

#left_entry? ⇒ Boolean

#

left_entry?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 244

def left_entry?
  @left_entry
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 441

def menu(
    i = commandline_arguments?
  )
  if i and i.is_a?(Array)
    if i.empty?
      set_dna_sequence(:default)
      update_the_left_entry
    else
      i.each {|entry| menu(entry) }
    end
  else
    case i # Perform some sanitizing here. (case tag)
    # ===================================================================== #
    # === ubiquitin
    # ===================================================================== #
    when 'ubiquitin',
         'ubi'
      i = ''
      set_these_aminoacids(
        ::Bioroebe.return_ubiquitin_sequence
      )
    else
      # =================================================================== #
      # Else we will simply assign the DNA sequence as-is. If the input
      # is a .fasta or .fasta file then we will use ParseFasta to obtain
      # the real sequence instead.
      # =================================================================== #
      assign_this_fasta_file(i)
      update_the_left_entry
    end
  end
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 119

def padding?
  8
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 79

def reset
  reset_the_internal_variables
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, NAMESPACE]
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
  infer_the_size_automatically
  set_border_width(15) if respond_to? :set_border_width
  signal_destroy_then_quit
  # ======================================================================= #
  # === @dna_sequence
  #
  # This is the dna sequence we will use. We will not work on the
  # entry directly, as this depends on gtk-initialization which
  # may not yet have happened.
  # ======================================================================= #
  @dna_sequence = :default
  # ======================================================================= #
  # === @aminoacid_sequence
  # ======================================================================= #
  @aminoacid_sequence = ''.dup
  # ======================================================================= #
  # === @parent_widget
  # ======================================================================= #
  @parent_widget = nil
  handle_CSS_rules
end

#right_entry? ⇒ Boolean

#

right_entry?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 269

def right_entry?
  @right_entry
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 605

def run
  super()
  menu
end

#sanitized_half_width ⇒ Object

#

sanitized_half_width

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 237

def sanitized_half_width
  (@width / 2) - 30
end

#set_aminoacid_sequence(i) ⇒ Object Also known as: set_these_aminoacids

#

set_aminoacid_sequence

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 508

def set_aminoacid_sequence(i)
  @aminoacid_sequence = i
end

#set_dna_sequence(i = left_entry?.text) ⇒ Object

#

set_dna_sequence

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 422

def set_dna_sequence(
    i = left_entry?.text
  )
  case i
  # ======================================================================= #
  # === :default
  # ======================================================================= #
  when :default
    i = 'ATG CGG'.dup
  end
  if i and i.start_with?('--')
    i = '' # Ad-hoc fix.
  end
  @dna_sequence = i.to_s.dup
end

#set_left_entry(i = @dna_sequence) ⇒ Object

#

set_left_entry

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 150

def set_left_entry(
    i = @dna_sequence
  )
  left_entry?.set_text(i)
end

#set_parent_widget(i) ⇒ Object

#

set_parent_widget

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 276

def set_parent_widget(i)
  @parent_widget = i
end

#set_right_entry(i = @aminoacid_sequence) ⇒ Object

#

set_right_entry

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 141

def set_right_entry(
    i = @aminoacid_sequence
  )
  right_entry?.set_text(i)
end

#sync_the_entries_back_onto_the_two_main_strings ⇒ Object

#

sync_the_entries_back_onto_the_two_main_strings

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 159

def sync_the_entries_back_onto_the_two_main_strings
  @dna_sequence       = return_the_main_DNA_sequence
  @aminoacid_sequence = right_entry?.text.to_s
end

#update_the_dna_sequence_then_do_the_conversion ⇒ Object

#

update_the_dna_sequence_then_do_the_conversion

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 283

def update_the_dna_sequence_then_do_the_conversion
  set_dna_sequence(
    left_entry?.text.upcase # Upcasing this is more elegant, in my opinion.
  )
  do_the_conversion
end

#update_the_entries ⇒ Object

#

update_the_entries

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 133

def update_the_entries
  set_left_entry
  set_right_entry
end

#update_the_left_entry ⇒ Object

#

update_the_left_entry

#

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# File 'lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 218

def update_the_left_entry
  set_left_entry(@dna_sequence.to_s)
end