Class: Bioroebe::GUI::UniversalWidgets::DnaToReverseComplementWidget

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

Overview

Bioroebe::GUI::UniversalWidgets::DnaToReverseComplementWidget

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this small widget.

#
'DNA to Reverse Complement'
WIDTH =
#

WIDTH

#
'65% or 500px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 300px minimum'
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
SMALLER_FONT =
#

SMALLER_FONT

#
:hack_16
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16

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) ⇒ DnaToReverseComplementWidget

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 73

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::DnaToReverseComplementWidget[]

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 452

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::DnaToReverseComplementWidget.run

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 459

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::DnaToReverseComplementWidget.new(i)
  )
  r.modify_background(:normal, :mintcream)
  return r
end

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 323

def border_size?
  0
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 409

def connect_the_skeleton
  abort_on_exception

  vbox = create_vbox

  @grid.left  @dna_sequence_label
  @grid.middle text('')
  @grid.right @reverse_complement_sequence_label
  @grid.left  @left_input_field_dna
  @grid.middle @event_box_containing_the_right_arrow
  @grid.right @right_input_field_aa
  @grid.full_row(
    @button_trigger_conversion,
    :default,
    :default,
    3
  )
  vbox.minimal(@grid)
  vbox.minimal(horizontal_separator)
  vbox.minimal(@label_n_nucleotides)

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

  ::UniversalWidgets.set_main_window(window)
  upon_delete_event_quit_the_application
  handle_commandline_arguments # This must come after the GUI skeleton was created.
  let_the_left_entry_react_to_enter_events

  window.use_this_font = font?
  window.show_all
  window.set_size_request(width?, height?)
  window.set_default_size(width?, height?)
  window.set_padding(padding?)
  window.set_border_size(border_size?)
  window.set_size_request(80, 100)
  window.top_left
  run_main
end

#consider_sanitizing_the_left_input_field_for_dna ⇒ Object

#

consider_sanitizing_the_left_input_field_for_dna

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 236

def consider_sanitizing_the_left_input_field_for_dna
  _ = @left_input_field_dna.text?.dup
  if _.include? 'U'
    _.tr!('U','T')
  end
  _.upcase!
  set_dna_sequence(_)
end

#create_button_trigger_conversion ⇒ Object

#

create_button_trigger_conversion

#


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

def create_button_trigger_conversion
  # ======================================================================= #
  # === @button_trigger_conversion
  # ======================================================================= #
  @button_trigger_conversion = bold_button('_Trigger Conversion', self, :use_mnemonics) {
    :do_sync_the_fields
  }
  @button_trigger_conversion.clear_background
  @button_trigger_conversion.set_background_colour :whitesmoke
  @button_trigger_conversion.on_hover(:lightgreen)
  @button_trigger_conversion.bblack1
  # ======================================================================= #
  # Use a tooltip as well for our button:
  # ======================================================================= #
  @button_trigger_conversion.hint = 
    "Clicking on this button will convert from a <b>DNA</b>\n"\
    "<b>sequence</b> to the <b>corresponding reverse "\
    "complement sequence</b>.\n\nMake sure you input the DNA sequence "\
    "on the left hand side."
end

#create_hbox_containing_the_two_input_fields ⇒ Object

#

create_hbox_containing_the_two_input_fields

This method will combine the two widgets.

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 301

def create_hbox_containing_the_two_input_fields
  
  # ========================================================================= #
  # In the middle will be a small arrow, though.
  # ========================================================================= #
  @hbox_containing_the_two_input_fields.maximal(@left_input_field_dna)
  if use_gtk3?
    @hbox_containing_the_two_input_fields.minimal(@event_box_containing_the_right_arrow)
  end
  @hbox_containing_the_two_input_fields.maximal(@right_input_field_aa)
end

#create_input_fields ⇒ Object

#

create_input_fields

These are the two input fields, also known as “gtk-entries”.

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 194

def create_input_fields
  # ======================================================================= #
  # The DNA widget, a gtk-entry widget.
  # ======================================================================= #
  @left_input_field_dna = input_field
  @left_input_field_dna.width_height(600, 20)
  @left_input_field_dna.very_light_yellowish_background
  @left_input_field_dna.hint = 'Input your DNA sequence here. Upon '\
    'clicking on the arrow or hitting the <b>enter</b> key, the sequence is '\
    'first converted to DNA, and then the reverse complement is '\
    'calculated. Afterwards the result is shown on the right input '\
    'field.'
  # ======================================================================= #
  # === The right widget.
  # ======================================================================= #
  @right_input_field_aa = input_field
  @right_input_field_aa.very_light_yellowish_background
  # ======================================================================= #
  # The AA widget. Will be highlighted on a click event.
  # ======================================================================= #
  if @right_input_field_aa.respond_to? :on_click_event
    @right_input_field_aa.on_click_event { :highlight_text }
  end
end

#create_the_event_box ⇒ Object

#

create_the_event_box

#


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

def create_the_event_box
  # ======================================================================= #
  # === @event_box_containing_the_right_arrow
  # ======================================================================= #
  @event_box_containing_the_right_arrow = create_eventbox(
    create_label(:arrow_right)
  )
  @event_box_containing_the_right_arrow.on_clicked {
    do_sync_the_fields
  }
end

#create_the_grid ⇒ Object

#

create_the_grid

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 397

def create_the_grid
  # ======================================================================= #
  # === @grid
  # ======================================================================= #
  @grid = default_grid
  @grid.set_column_spacing(6)
  @grid.set_row_spacing(6)
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 359

def create_the_skeleton
  @label_n_nucleotides = text
  create_input_fields
  # ======================================================================= #
  # === @dna_sequence_label
  # ======================================================================= #
  @dna_sequence_label = return_dna_sequence_label
  create_the_grid
  create_the_event_box
  create_button_trigger_conversion
  create_the_top_labels
end

#create_the_top_labels ⇒ Object

#

create_the_top_labels

The two top labels denote which widget is the one for the DNA sequence, and which one is for the aminoacid sequence.

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 153

def create_the_top_labels
  @dna_sequence_label = return_dna_sequence_label
  @reverse_complement_sequence_label = return_reverse_complement_to_that_dna_sequence
end

#do_sync_the_fields ⇒ Object

#

do_sync_the_fields

This method will sync between the two main widgets - the DNA input field on the left, and the reverse complement on the right side.

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 110

def do_sync_the_fields
  consider_sanitizing_the_left_input_field_for_dna
  _ = @left_input_field_dna.text?
  if ::Bioroebe.const_defined? :Controller
    # ===================================================================== #
    # Ok, in this case we can store the dataset via a class-method.
    # ===================================================================== #
    ::Bioroebe::GUI::Controller.set_dna_sequence(_)
  end
  # ======================================================================= #
  # Next, we must translate from DNA to the reverse complement sequence.
  # ======================================================================= #
  _ = ::Bioroebe.complement(_)
  set_reverse_complement(_.reverse)
  n_nucleotides = _.size
  @label_n_nucleotides.set_text(
    'This DNA sequence contains <b>'+n_nucleotides.to_s+'</b> nucleotides.'
  )
  @label_n_nucleotides.do_markify
end

#favicon? ⇒ Boolean

#

favicon?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 222

def favicon?
  :tabble
end

#handle_commandline_arguments ⇒ Object

#

handle_commandline_arguments

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 289

def handle_commandline_arguments
  input = input?
  if input and !input.empty? and !input.include?('--') # Reject commandline-arguments, though.
    set_dna_sequence(input)
  end
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/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 344

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

 grid {
    padding: 20px;
  }
  '
  apply_the_CSS_rules
end

#input? ⇒ Boolean

#

input?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 282

def input?
  @input
end

#let_the_left_entry_react_to_enter_events ⇒ Object

#

let_the_left_entry_react_to_enter_events

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 141

def let_the_left_entry_react_to_enter_events
  @left_input_field_dna.on_enter {
    do_sync_the_fields unless @left_input_field_dna.text?.empty?
  }
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 330

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 316

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#


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

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?
end

#return_dna_sequence_label ⇒ Object

#

return_dna_sequence_label

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 134

def return_dna_sequence_label
  bold_label('DNA sequence')
end

#return_reverse_complement_to_that_dna_sequence ⇒ Object

#

return_reverse_complement_to_that_dna_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 161

def return_reverse_complement_to_that_dna_sequence
  bold_label('Reverse complement to that DNA sequence')
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 375

def run
  run_super
end

#set_dna_sequence(i = input? ) ⇒ Object

#

set_dna_sequence

This method will set to the input-field on the left hand side.

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 250

def set_dna_sequence(
    i = input?
  )
  if i.is_a? Array
    i = i.join(' ').strip
  end
  unless i.include?('--') # Reject commandline-arguments, though.
    @left_input_field_dna.set_text(i)
  end
end

#set_input(i = '') ⇒ Object

#

set_input

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 264

def set_input(i = '')
  i = i.first if i.is_a? Array
  i = i.to_s.dup
  case i # Perform some sanitizing here. (case tag)
  # ======================================================================= #
  # === ubiquitin
  # ======================================================================= #
  when 'ubiquitin',
       'ubi'
    i = ''
    set_these_aminoacids(::Bioroebe.return_ubiquitin_sequence)
  end
  @input = i
end

#set_reverse_complement(i) ⇒ Object

#

set_reverse_complement

#


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 229

def set_reverse_complement(i)
  @right_input_field_aa.set_text(i)
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb', line 337

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end