Class: Bioroebe::GUI::UniversalWidgets::AntiSenseStrand

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

Overview

Bioroebe::GUI::UniversalWidgets::AntiSenseStrand

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this small widget.

#
'Sense / Anti-Sense Strand'
WIDTH =
#

WIDTH

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

HEIGHT

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

TEXT_COMPARE_THE_TWO_SEQUENCES

#
'_Compare the two sequences'
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
MAX_LENGTH =
#

MAX_LENGTH

#
50_000
IMG_DNA_HELIX =
#

IMG_DNA_HELIX

#
'/home/x/data/images/science/biology/DNA_HELIX.jpg'
SMALLER_FONT =
#

SMALLER_FONT

#
:hack_16
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16
USE_THIS_TITLE_FOR_THE_MAIN_BUTTON =
#

USE_THIS_TITLE_FOR_THE_MAIN_BUTTON

#
'_Determine the DNA sequence'
PADDING_TO_USE =
#

PADDING_TO_USE

#
12
DEFAULT_TEXT_FOR_ENTRY1 =
#

DEFAULT_TEXT_FOR_ENTRY1

#
'AGUUCGAUGGAAAATAT'
DEFAULT_TEXT_FOR_ENTRY2 =
#

DEFAULT_TEXT_FOR_ENTRY2

#
'AGUCCGGUCGAAAAAAA'

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) ⇒ AntiSenseStrand

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 114

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::AntiSenseStrand[]

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 643

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::AntiSenseStrand.run

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 650

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

Instance Method Details

#aminoacid_sequence? ⇒ Boolean

#

aminoacid_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 425

def aminoacid_sequence?
  left_buffer?.to_s
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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

def border_size?
  8
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 590

def connect_the_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.make_selectable
  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)

  Thread.new {
    sleep 0.01
    @entry_n_differences.do_focus
    entry1?.deselect
    do_compare
  }

  window = runner_widget(nil, width?, height?, title?)
  window << vpaned
  ::UniversalWidgets.set_main_window(window)
  upon_delete_event_quit_the_application
  jump_into_the_first_entry
  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_input ⇒ Object

#

consider_sanitizing_the_input

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 560

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

#consider_sanitizing_the_input_and_then_compare_the_two_sequences ⇒ Object

#

consider_sanitizing_the_input_and_then_compare_the_two_sequences

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 477

def consider_sanitizing_the_input_and_then_compare_the_two_sequences
  consider_sanitizing_the_input
  compare_the_two_sequences
end

#create_buttons ⇒ Object

#

create_buttons (buttons tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 367

def create_buttons
  backtrack_button = bold_button(
    USE_THIS_TITLE_FOR_THE_MAIN_BUTTON, self, :use_mnemonic
  ) {
    :do_determine_the_backtrack_sequence
  }
  backtrack_button.set_name('button1')
  backtrack_button.do_use_underline
  backtrack_button.hint = 
    "On the <b>left hand side</b>, you should input the "\
    "Aminoacid sequence.\n\n"\
    "On the <b>right hand side</b>, a possible DNA "\
    "sequence for this Aminoacid Sequence will "\
    "be displayed.\n\n"\
    "Invalid amino acids, such as 'U', will be filtered "\
    "out, if given.\n\n"\
    "Note that this will not necessarily "\
    "generate the same sequence, due to several different codons "\
    "encoding for the same aminoacid."
  backtrack_button.on_hover_lightblue
  @dataset[:backtrack_button] = backtrack_button
  a_quit_button = quit_button
  a_quit_button.set_name('button1')
  a_quit_button.make_bold
  @dataset[:quit_button] = a_quit_button
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/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 459

def create_compare_button
  # ======================================================================= #
  # === @compare_button
  # ======================================================================= #
  @compare_button = bold_button(TEXT_COMPARE_THE_TWO_SEQUENCES, self, :use_mnemonics) {
    :consider_sanitizing_the_input_and_then_compare_the_two_sequences
  }
  @compare_button.apply_markup
  @compare_button.on_hover(:lightblue)
  @compare_button.set_name('button1')
  @compare_button.hint = 'Click this button to '\
    '<span weight="bold" foreground="lightblue">compare</span> '\
    'the two sequences.'
end

#create_left_buffer ⇒ Object

#

create_left_buffer

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 308

def create_left_buffer
  # ======================================================================= #
  # === :left_buffer
  # ======================================================================= #
  @dataset[:left_buffer] = create_text_view # The left text view.
  @dataset[:left_buffer].bblack1
  @dataset[:left_buffer].do_wrap_properly
end

#create_middle_bar_containing_the_arrow_pointing_to_the_right_side ⇒ Object

#

create_middle_bar_containing_the_arrow_pointing_to_the_right_side

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 259

def create_middle_bar_containing_the_arrow_pointing_to_the_right_side
  @middle_bar = create_vbox
  event_box = create_eventbox(
    create_label(:arrow_right)
  )
  event_box.hint =
    'This arrow can be clicked, to convert from the aminoacid sequence '\
    'to (one likely) possible DNA sequence.'
  event_box.on_clicked {
    do_determine_the_backtrack_sequence
  }
  @middle_bar.minimal(
    event_box
  )
end

#create_right_buffer ⇒ Object

#

create_right_buffer

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 149

def create_right_buffer
  # ======================================================================= #
  # === :right_buffer
  # ======================================================================= #
  @dataset[:right_buffer] = create_text_view # The right text view.
  @dataset[:right_buffer].bblack1
  @dataset[:right_buffer].do_wrap_properly
end

#create_the_entries ⇒ Object

#

create_the_entries (entries tag, entry tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 196

def create_the_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 = 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 = create_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 = create_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_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 485

def create_the_skeleton
  create_the_entries
  # ======================================================================= #
  # === The top box
  # ======================================================================= #
  @top_box = vbox

  @label_on_top = bold_label(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 = create_hbox
  @hbox_for_string1.minimal(text('1').make_bold, 1)
  @hbox_for_string1.maximal(@entry_on_top, 1)

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

  create_compare_button

  small_hbox = create_hbox
  # ======================================================================= #
  # === n_differences found Gtk::Text
  # ======================================================================= #
  short_text_widget = 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 = create_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

#create_top_hbox ⇒ Object

#

create_top_hbox

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 278

def create_top_hbox
  # ======================================================================= #
  # The paned-widget is close to the top.
  # ======================================================================= #
  scrolled_window_right = scrolled_window(right_buffer?)
  scrolled_window_right.clear_background
  scrolled_window_right.width_height(300, 300)
  scrolled_window_right.bblack1
  scrolled_window_right.mar2px
  # ======================================================================= #
  # === scrolled_window_left
  # ======================================================================= #
  scrolled_window_left  = scrolled_window(left_buffer?)
  scrolled_window_left.clear_background
  scrolled_window_left.width_height(300, 300)
  scrolled_window_left.bblack1
  scrolled_window_left.mar2px
  top_hpaned = gtk_hpaned(
    scrolled_window_left,
    scrolled_window_right
  ) {{ border_width: 10 }}
  this_position = (width?.to_f / 1.5).to_i
  top_hpaned.set_position(this_position)
  top_hpaned.show_all
  @dataset[:top_hbox] = top_hpaned
end

#do_determine_the_backtrack_sequence ⇒ Object Also known as: do_determine_the_DNA_sequence

#

do_determine_the_backtrack_sequence (click tag)

This will do what is necessary to find the backtrack sequence.

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 441

def do_determine_the_backtrack_sequence
  filter_away_invalid_aminoacids_from_the_left_buffer
  _ = left_buffer?.text?.to_s
  _.upcase!
  _ = ::Bioroebe.remove_invalid_aminoacids(_)
  left_buffer?.set_text(_)
  # ======================================================================= #
  # Ok, now we can determine the right hand side:
  # ======================================================================= #
  text_for_right_hand_side = ::Bioroebe::ProteinToDNA.new(_, :be_quiet).dna_sequence?
  right_buffer?.set_text(text_for_right_hand_side)
end

#do_upcase_all_entries ⇒ Object

#

do_upcase_all_entries

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 548

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

#entry1? ⇒ Boolean Also known as: entry1

#

entry1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 189

def entry1?
  @entry_on_top
end

#filter_away_invalid_aminoacids_from_the_left_buffer ⇒ Object

#

filter_away_invalid_aminoacids_from_the_left_buffer

This method is used to “sanitize” the input - invalid aminoacids are flat out removed.

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 400

def filter_away_invalid_aminoacids_from_the_left_buffer
  _ = left_buffer?.text?.to_s
  possible_new_text = Bioroebe.strict_filter_away_invalid_aminoacids(_)
  unless _ == possible_new_text
    left_buffer?.set_text(possible_new_text)
  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/anti_sense_strand/anti_sense_strand.rb', line 334

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

#custom_treeview.view header button {
background-color: white;
color: royalblue;
font-weight: bold;
font-size: larger;
padding: 8px;
}'
  apply_the_CSS_rules
end

#jump_into_the_first_entry ⇒ Object

#

jump_into_the_first_entry

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 636

def jump_into_the_first_entry
  entry1?.do_focus
end

#left_buffer? ⇒ Boolean Also known as: left?

#

left_buffer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 432

def left_buffer?
  @dataset[:left_buffer]
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 320

def main_font?
  USE_THIS_FONT
end

#menu(i = nil) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 352

def menu(i = nil)
  if i
    if i.is_a? Array
      i.each {|entry| menu(entry) }
    else
      case i # case tag
      when ''
      end
    end
  end
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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

def padding?
  PADDING_TO_USE
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 129

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?
  set_border_width(5)
end

#right_buffer? ⇒ Boolean Also known as: right?

#

right_buffer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 411

def right_buffer?
  @dataset[:right_buffer]
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 534

def run
  run_super
end

#seq1? ⇒ Boolean

#

seq1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 175

def seq1?
  @entry_on_top.text
end

#seq2? ⇒ Boolean

#

seq2?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 182

def seq2?
  @entry_on_bottom.text
end

#set_aminoacid_sequence(i) ⇒ Object

#

set_aminoacid_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 418

def set_aminoacid_sequence(i)
  @dataset[:left_buffer].set_text(i.to_s)
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 327

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#synchronize_anti_sense ⇒ Object

#

synchronize_anti_sense

Will fetch content and synchronize the @entry_anti_sense

#


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 574

def synchronize_anti_sense
  this_text = ''.dup
  @entry_sense.text?.each_char { |char|
    case char
    when 'A' then this_text << 'T'
    when 'T' then this_text << 'A'
    when 'C' then this_text << 'G'
    when 'G' then this_text << 'C'
    end
  }
  @entry_anti_sense.set_text(this_text)
end

#top_hbox? ⇒ Boolean

#

top_hbox?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/anti_sense_strand/anti_sense_strand.rb', line 541

def top_hbox?
  @dataset[:top_hbox]
end