Class: Bioroebe::GUI::Gtk::HammingDistance

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

Overview

Bioroebe::GUI::Gtk::HammingDistance

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
WIDTH =
#

WIDTH

#
500
HEIGHT =
#

HEIGHT

#
320
TITLE =
#

TITLE

Specify which title to use for this small widget.

#
'Hamming Distance'
USE_THIS_TITLE =

USE_THIS_TITLE

TITLE
PADDING_TO_USE =
#

PADDING_TO_USE

#
5
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
DEFAULT_TEXT_FOR_ENTRY1 =
#

DEFAULT_TEXT_FOR_ENTRY1

#
'AGUUCGAUGGAAAATAT'
DEFAULT_TEXT_FOR_ENTRY2 =
#

DEFAULT_TEXT_FOR_ENTRY2

#
'AGUCCGGUCGAAAAAAA'

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(optional_commandline_arguments = nil, run_already = true) ⇒ HammingDistance

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 82

def initialize(
    optional_commandline_arguments = nil,
    run_already                    = true
  )
  super(:horizontal)
  register_sigint
  reset
  set_title(USE_THIS_TITLE) if respond_to?(:set_title)
  if optional_commandline_arguments and respond_to?(:menu)
    menu(optional_commandline_arguments)
  end
  signal_destroy_then_quit
  run if run_already
end

Class Method Details

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::HammingDistance.run

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 368

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

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 123

def border_size?
  0
end

#compare_the_two_sequences ⇒ Object Also known as: do_compare, do_calculate_the_differences

#

compare_the_two_sequences

This is the method that will compare the two sequences.

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 318

def compare_the_two_sequences
  do_upcase_all_entries
  hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
  @entry_n_differences.set_text(
    hamming_distance_object.n_differences?.to_s
  )
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 292

def connect_skeleton
  abort_on_exception
  # ======================================================================= #
  # @top_box is an instance of gtk-vbox.
  # ======================================================================= #
  @top_box.minimal(@label_on_top,     1)
  text = left_aligned_text(
      "The <b>Hamming distance</b> - a number - measures the number of "\
      "\npositions at which two strings of equal length are "\
      "different.")
  text.use_this_font = SMALLER_FONT
  @top_box.minimal(text,              12)
  @top_box.minimal(@hbox_for_string1,  2)
  @top_box.minimal(@hbox_for_string2,  2)

  vpaned = mouse_draggable_via_up_and_down_movement(@top_box, @bottom_box)
  vpaned.set_size_request(@width, 550)
  maximal(vpaned, 8)
  show_all
end

#consider_sanitizing_the_input ⇒ Object

#

consider_sanitizing_the_input

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 342

def consider_sanitizing_the_input
  # ======================================================================= #
  # The following two lines were added as of 07.05.2020.
  # ======================================================================= #
  @entry_on_top.set_text(@entry_on_top.text.delete('-'))
  @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
  do_upcase_all_entries
end

#create_compare_button ⇒ Object

#

create_compare_button

This method will create the button that will compare the two sequences.

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 223

def create_compare_button
  # ======================================================================= #
  # === @compare_button
  # ======================================================================= #
  @compare_button = bold_button(::Bioroebe::GUI::LevenstheinDistanceModule::TEXT_COMPARE_THE_TWO_SEQUENCES)
  @compare_button.apply_markup
  @compare_button.lightblue
  @compare_button.set_name('button1')
  @compare_button.hint = 'Click this button to '\
    '<span weight="bold" foreground="lightblue">compare</span> '\
    'the two sequences.'
  @compare_button.on_clicked {
    consider_sanitizing_the_input
    compare_the_two_sequences
  }
end

#create_entries ⇒ Object

#

create_entries (entries tag, entry tag)

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 158

def create_entries
  # ======================================================================= #
  # === @entry_n_differences
  #
  # This is the entry that will simply show the number of differences
  # between the two sequences, as a number.
  # ======================================================================= #
  @entry_n_differences = gtk_entry_with_icon_name('edit-undo-symbolic-rtl.symbolic')
  @entry_n_differences.xalign = 0.5 # Align towards the center.
  @entry_n_differences.bblack1
  @entry_n_differences.clear_background
  @entry_n_differences.yellow_background

  # ======================================================================= #
  # === @entry_on_top
  # ======================================================================= #
  @entry_on_top = gtk_entry(DEFAULT_TEXT_FOR_ENTRY1)
  @entry_on_top.set_font(MONOSPACED_FONT)
  @entry_on_top.clear_background
  @entry_on_top.css_class('BG_lightsteelblue')
  @entry_on_top.bblack1
  @entry_on_top.on_changed { do_calculate_the_differences }
  @entry_on_top.hint = 'This entry should contain the first sequence (seq1).'
  @entry_on_top.set_max_length(50_000)
  @entry_on_top.on_key_press_event { |widget, event|
    old_text = widget.text
    keyname = Gdk::Keyval.to_name(event.keyval)
    case keyname.upcase
    when *%w( A T C G U )
      # This is ok.
    when *%w( B D E F H I J K L M N O P Q R S V W X Y Z ) # Otherwise set the old input here.
      unless event.state.control_mask? # This snippet checks whether a key-combination has been used.
        widget.set_text(old_text.upcase)
      end
    end
  } if false # disabled as of August 2022.
  # ======================================================================= #
  # And keep things upcased here:
  # ======================================================================= #
  @entry_on_top.on_key_release { |widget, event|
    old_text = @entry_on_top.text
    new_text = @entry_on_top.text.upcase
    unless old_text == new_text
      @entry_on_top.set_text(new_text)
      @entry_on_top.move_cursor_to_the_most_right_position
    end
  }

  # ======================================================================= #
  # === @entry_on_bottom
  # ======================================================================= #
  @entry_on_bottom = gtk_entry(DEFAULT_TEXT_FOR_ENTRY2)
  @entry_on_bottom.set_font(MONOSPACED_FONT)
  @entry_on_bottom.css_classes('clear_background BG_lightsteelblue')
  @entry_on_bottom.bblack1
  @entry_on_bottom.on_changed { do_calculate_the_differences }
  @entry_on_bottom.hint = 'This entry should contain the second sequence (seq2).'
  @entry_on_bottom.set_max_length(50_000)
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag, skeleton tag)

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 243

def create_skeleton
  create_entries
  # ======================================================================= #
  # === The top box
  # ======================================================================= #
  @top_box = vbox

  @label_on_top = bold_label(USE_THIS_TITLE)
  @label_on_top.hint = 
    "Only <b>valid nucleotides</b> (A, T, C, G, U) \n"\
    "can be accepted as input."
  # ======================================================================= #
  # Create the top hbox for string1 next:
  # ======================================================================= #
  @hbox_for_string1 = gtk_hbox
  @hbox_for_string1.minimal(gtk_label('1').make_bold, 1)
  @hbox_for_string1.maximal(@entry_on_top, 1)

  # ======================================================================= #
  # Create the bottom hbox for string2 next:
  # ======================================================================= #
  @hbox_for_string2 = gtk_hbox
  @hbox_for_string2.minimal(gtk_label('2').make_bold, 1)
  @hbox_for_string2.maximal(@entry_on_bottom, 1)

  create_compare_button

  small_hbox = gtk_hbox
  # ======================================================================= #
  # === n_differences found Gtk::Text
  # ======================================================================= #
  short_text_widget = gtk_text('<b>n differences</b> found:')
  short_text_widget.do_markify
  small_hbox.minimal(short_text_widget, 2)
  small_hbox.hint =
    'This entry will show <b>how many differences</b> '\
    'exist between these two strings.'
  small_hbox.minimal(@entry_n_differences, 2)
  # ======================================================================= #
  # === The bottom box
  # ======================================================================= #
  @bottom_box = gtk_vbox
  @bottom_box.pack_start(@compare_button, expand: false, fill: false, padding: 1)
  @bottom_box.pack_start(small_hbox, expand: false, fill: true, padding: 0)
end

#do_upcase_all_entries ⇒ Object

#

do_upcase_all_entries

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 330

def do_upcase_all_entries
  [
    @entry_on_top,
    @entry_on_bottom
  ].each {|entry|
    entry.do_upcase
  }
end

#entry1? ⇒ Boolean

#

entry1?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 151

def entry1?
  @entry_on_top
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 116

def padding?
  PADDING_TO_USE
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 100

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
  set_border_width(5) 
  infer_the_size_automatically
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 354

def run
  create_skeleton_then_connect_skeleton
  set_minimum_size
  Thread.new {
    sleep 0.01
    @entry_n_differences.do_focus
    entry1?.deselect
    do_compare
  }
end

#seq1? ⇒ Boolean

#

seq1?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 130

def seq1?
  @entry_on_top.text
end

#seq2? ⇒ Boolean

#

seq2?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 137

def seq2?
  @entry_on_bottom.text
end

#set_minimum_size ⇒ Object

#

set_minimum_size

#

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# File 'lib/bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb', line 144

def set_minimum_size
  set_size_request(80, 100)
end