Class: Bioroebe::GUI::UniversalWidgets::LevenstheinDistance

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

Overview

Bioroebe::GUI::UniversalWidgets::LevenstheinDistance

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
'Levensthein Distance'
WIDTH =
#

WIDTH

#
'75% or 900px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 440px minimum'
FONT_LARGE =
#

FONT_LARGE

#
'Calibri 32'
MONOSPACED_FONT =
#

MONOSPACED_FONT

When this font is changed, don’t forget to also change the font at SMALLER_FONT.

#
:hack_22
USE_THIS_FONT = 
MONOSPACED_FONT
USE_THIS_MONOFONT = 
MONOSPACED_FONT
SMALLER_FONT =
#

SMALLER_FONT

#
:hack_16
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16
USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET =
#

USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET

This constant can be used to designate the background colour to be used for the widget.

#
:white
INPUT_HINT =
#

INPUT_HINT

#
"Hit the enter-key to compare the two sequences. Don't forget to "\
"assign two sequences first, e. g. ATG and then ATT, as an example."
TEXT_COMPARE_THE_TWO_SEQUENCES =
#

Bioroebe::GUI::LevenstheinDistanceModule::TEXT_COMPARE_THE_TWO_SEQUENCES

#
'_Compare the two sequences'

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) ⇒ LevenstheinDistance

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 101

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::LevenstheinDistance[]

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 607

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::LevenstheinDistance.run

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 614

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::LevenstheinDistance.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/levensthein_distance/levensthein_distance.rb', line 143

def border_size?
  4
end

#check_for_commandline_arguments(commandline_arguments = commandline_arguments? ) ⇒ Object Also known as: parse_the_commandline_arguments

#

check_for_commandline_arguments

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 496

def check_for_commandline_arguments(
    commandline_arguments = commandline_arguments?
  )
  if commandline_arguments and commandline_arguments.is_a?(Array)
    unless commandline_arguments.empty?
      set_entry1(commandline_arguments[0])
      set_entry2(commandline_arguments[1])
    end
  end
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 539

def connect_the_skeleton
  abort_on_exception

  vbox1 = create_vbox
  populate_the_grid
  vbox1.minimal(@grid, 4)
  if levensthein_object?.sequence1?
    unless levensthein_object?.sequence1?.empty?
      @input_for_string1.set_text(levensthein_object?.sequence1?)
    end
  end
  if levensthein_object?.sequence2?
    unless levensthein_object?.sequence2?.empty?
      @input_for_string2.set_text(levensthein_object?.sequence2?)
    end
  end
  vbox1.minimal(@input_for_string1, 4)
  vbox1.minimal(@input_for_string2, 4)
  # ======================================================================= #
  # Next below these two input-fields we will add more info:
  # ======================================================================= #
  small_label = return_the_edit_distance_label
  @hbox_with_the_label_for_the_edit_distance = return_hbox_containing_the_edit_distance(
    small_label, @label_for_the_edit_distance
  )
  @hbox4 = return_hbox4(
    @label_for_the_total_score
  )
  vbox1.minimal(@hbox_with_the_label_for_the_edit_distance, 4)
  vbox1.minimal(@hbox4, 4)
  button_box = create_button_box(
    @button_compare_the_two_strings
  ) { :spread }
  vbox1.minimal(button_box, 4)

  window = runner_widget(nil, width?, height?, title?)
  window << vbox1
  
  check_for_commandline_arguments
  do_compare_the_two_sequences
  let_the_fist_entry_respond_to_on_changed_events

  ::UniversalWidgets.set_main_window(window)
  jump_into_the_first_entry
  upon_delete_event_quit_the_application
  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.modify_background(
    :normal, USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET
  )
  window.top_left
  run_main
end

#create_the_buttons ⇒ Object

#

create_the_buttons

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 271

def create_the_buttons
  # ======================================================================= #
  # === @button_compare_the_two_strings
  # ======================================================================= #
  @button_compare_the_two_strings = bold_button(
    TEXT_COMPARE_THE_TWO_SEQUENCES, self, :use_mnemonics
  ) {
    do_compare_the_two_strings
  }
  @button_compare_the_two_strings.clear_background
  @button_compare_the_two_strings.set_size_request(200, 40)
  @button_compare_the_two_strings.set_border_width(4)
  @button_compare_the_two_strings.bblack2
  @button_compare_the_two_strings.hint =
    'Click to compare the two sequences. Ideally use the '\
    '<b>same length</b> for the two sequences. Make sure to '\
    'click it once more after you are done, as the auto-calculation '\
    'currently does NOT take the second entry into '\
    'consideration.'
  @button_compare_the_two_strings.on_hover(:lightcyan) 
end

#create_the_entries ⇒ Object

#

create_the_entries (entries tag, entry tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 510

def create_the_entries
  # ======================================================================= #
  # Next, add the two input-fields for our two nucleotide sequences.
  # ======================================================================= #
  # ======================================================================= #
  # === @input_for_string1
  # ======================================================================= #
  @input_for_string1 = input
  @input_for_string1.light_green_background
  @input_for_string1.bblack1
  @input_for_string1.css_class('pad4px')
  @input_for_string1.on_enter { do_compare_the_two_strings }
  @input_for_string1.use_this_font = USE_THIS_MONOFONT
  @input_for_string1.hint = INPUT_HINT
  # ======================================================================= #
  # === @input_for_string2
  # ======================================================================= #
  @input_for_string2 = input
  @input_for_string2.light_green_background
  @input_for_string2.bblack1
  @input_for_string2.css_class('pad4px')
  @input_for_string2.on_enter { do_compare_the_two_strings }
  @input_for_string2.use_this_font = USE_THIS_MONOFONT
  @input_for_string2.hint = INPUT_HINT
end

#create_the_first_row ⇒ Object

#

create_the_first_row

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 318

def create_the_first_row
  # ======================================================================= #
  # === @text1
  # ======================================================================= #
  @text1 = bold_text_left_aligned('Score for match (match cost): ')
  @text1.make_selectable
  # ======================================================================= #
  # === @input_field_for_matches
  # ======================================================================= #
  @input_field_for_matches = spinbutton(-50, 150)
  @input_field_for_matches.bblack1
  @input_field_for_matches.center
  @input_field_for_matches.yellow_background
  @input_field_for_matches.set_size_request(100, 40)
  @input_field_for_matches.set_value(
    levensthein_object?.score_for_match?.to_s.to_i
  )
  @input_field_for_matches.align_to_center
  @input_field_for_matches.on_changed {
    recalculate_the_score
  }
end

#create_the_grid ⇒ Object

#

create_the_grid (grid tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 150

def create_the_grid
  # ======================================================================= #
  # === @grid
  # ======================================================================= #
  @grid = create_grid
  @grid.set_column_spacing(4)
  @grid.set_row_spacing(4)
end

#create_the_labels ⇒ Object

#

create_the_labels

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 365

def create_the_labels
  # ======================================================================= #
  # === @label_for_the_total_score
  # ======================================================================= #
  @label_for_the_total_score = text('0')
  @label_for_the_total_score.use_this_font = USE_THIS_MONOFONT
  @label_for_the_total_score.make_bold
  @label_for_the_total_score.make_selectable
  # ======================================================================= #
  # === @label_for_the_edit_distance
  # ======================================================================= #
  @label_for_the_edit_distance = return_the_label_for_the_edit_distance
end

#create_the_second_row ⇒ Object

#

create_the_second_row

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 415

def create_the_second_row
  # ======================================================================= #
  # === Score for mismatch
  # ======================================================================= #
  @text2 = bold_text_left_aligned('Score for mismatch (mismatch cost): ')
  @text2.make_selectable
  # ======================================================================= #
  # === @input_field_for_mismatches
  # ======================================================================= #
  @input_field_for_mismatches = spinbutton(-50, 150)
  @input_field_for_mismatches.center
  @input_field_for_mismatches.yellow_background
  @input_field_for_mismatches.bblack1
  @input_field_for_mismatches.set_size_request(100, 40)
  @input_field_for_mismatches.set_value(
    levensthein_object?.score_for_mismatch?.to_s.to_i
  )
  @input_field_for_mismatches.align_to_center
  @input_field_for_mismatches.on_changed {
    recalculate_the_score
  }
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 199

def create_the_skeleton
  create_the_entries
  create_the_labels
  create_the_grid
  create_the_first_row
  create_the_second_row
  create_the_third_row
  create_the_buttons
end

#create_the_third_row ⇒ Object

#

create_the_third_row

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 296

def create_the_third_row
  # ======================================================================= #
  # === @text3
  # ======================================================================= #
  @text3 = bold_text_left_aligned(
    'Score for gap (gap cost): '
  )
  @input_field_for_gap_cost = spinbutton(-50, 150)
  @input_field_for_gap_cost.yellow_background
  @input_field_for_gap_cost.bblack1
  @input_field_for_gap_cost.set_value(
    levensthein_object?.score_for_gaps?.to_s.to_i
  )
  @input_field_for_gap_cost.align_to_center
  @input_field_for_gap_cost.on_changed {
    recalculate_the_score
  }
end

#do_compare_the_two_strings(text1 = entry1?.text?, text2 = entry2?.text?) ⇒ Object Also known as: do_compare_the_two_sequences, recalculate_the_score

#

do_compare_the_two_strings (click tag)

This is the main action of the widget.

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 443

def do_compare_the_two_strings(
    text1 = entry1?.text?,
    text2 = entry2?.text?
  )
  # ======================================================================= #
  # First capitalize the two entries:
  # ======================================================================= #
  entry1?.set_text(text1.upcase)
  entry2?.set_text(text2.upcase)
  @levensthein_object.reset_the_score
  @levensthein_object.set_match_score(@input_field_for_matches.text?)
  @levensthein_object.set_mismatch_score(@input_field_for_mismatches.text?)
  @levensthein_object.set_gap_score(input_field_for_gap_cost?.text?)
  @levensthein_object.set_string1(text1)
  @levensthein_object.set_string2(text2)
  @levensthein_object.run
  set_edit_distance(
    @levensthein_object.edit_distance?
  )
  total_score = @levensthein_object.total_score?.to_s
  unless text2.empty?
    @label_for_the_total_score.set_text(total_score)
    @label_for_the_total_score.make_bold
  end
end

#entry1? ⇒ Boolean Also known as: entry1, entry?

#

entry1?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 389

def entry1?
  @input_for_string1
end

#entry2? ⇒ Boolean

#

entry2?

#

Returns:

  • (Boolean) 


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

def entry2?
  @input_for_string2
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/levensthein_distance/levensthein_distance.rb', line 188

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
'
  apply_the_CSS_rules
end

#input_field_for_gap_cost? ⇒ Boolean

#

input_field_for_gap_cost?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 245

def input_field_for_gap_cost?
  @input_field_for_gap_cost
end

#instantiate_a_new_levensthein_object ⇒ Object

#

instantiate_a_new_levensthein_object

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 219

def instantiate_a_new_levensthein_object
  # ======================================================================= #
  # === @levensthein_object
  # ======================================================================= #
  @levensthein_object = ::Bioroebe::Levensthein.new(:dont_run_yet) {
    :be_quiet
  }
end

#jump_into_the_first_entry ⇒ Object

#

jump_into_the_first_entry

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 600

def jump_into_the_first_entry
  entry1?.do_focus
end

#let_the_fist_entry_respond_to_on_changed_events(widget_to_use = @input_for_string1) ⇒ Object

#

let_the_fist_entry_respond_to_on_changed_events

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 404

def let_the_fist_entry_respond_to_on_changed_events(
    widget_to_use = @input_for_string1
  )
  widget_to_use.on_changed {
    do_compare_the_two_sequences
  }
end

#levensthein_object? ⇒ Boolean Also known as: levensthein

#

levensthein_object?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 231

def levensthein_object?
  @levensthein_object
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 174

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 136

def padding?
  12
end

#populate_the_grid ⇒ Object

#

populate_the_grid

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 162

def populate_the_grid
  @grid.left(@text1)
  @grid.right(@input_field_for_matches)
  @grid.left(@text2)
  @grid.right(@input_field_for_mismatches)
  @grid.left(@text3)
  @grid.right(@input_field_for_gap_cost)
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 116

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?
  instantiate_a_new_levensthein_object
end

#return_hbox4(label_for_the_total_score = @label_for_the_total_score) ⇒ Object

#

return_hbox4

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 344

def return_hbox4(
    label_for_the_total_score = @label_for_the_total_score
  )
  # ======================================================================= #
  # === Total score: label
  # ======================================================================= #
  small_label_for_total_score = bold_label('Total score:     ')
  small_label_for_total_score.make_selectable
  # ======================================================================= #
  # === @hbox4
  # ======================================================================= #
  hbox4 = hbox(
    small_label_for_total_score,
    label_for_the_total_score
  )
  return hbox4 
end

#return_hbox_containing_the_edit_distance(small_label, label_for_the_edit_distance) ⇒ Object

#

return_hbox_containing_the_edit_distance

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 484

def return_hbox_containing_the_edit_distance(
    small_label,
    label_for_the_edit_distance
  )
  return hbox(
    small_label, label_for_the_edit_distance
  )
end

#return_the_edit_distance_label ⇒ Object

#

return_the_edit_distance_label

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 473

def return_the_edit_distance_label
  small_label = bold_label('Edit distance: ')
  small_label.make_selectable
  small_label.hint = 'This number tells us how many differences '\
                     'exist between the two sequences at hand.'
  return small_label
end

#return_the_label_for_the_edit_distance ⇒ Object

#

return_the_label_for_the_edit_distance

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 261

def return_the_label_for_the_edit_distance
  label_for_the_edit_distance = text('0')
  label_for_the_edit_distance.use_this_font = USE_THIS_MONOFONT
  label_for_the_edit_distance.make_bold
  return label_for_the_edit_distance
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 212

def run
  run_super
end

#set_edit_distance(i) ⇒ Object

#

set_edit_distance

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 252

def set_edit_distance(i)
  i = i.to_s
  @label_for_the_edit_distance.set_text(i.rjust(2))
  @label_for_the_edit_distance.make_bold
end

#set_entry1(i) ⇒ Object

#

set_entry1

#


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

def set_entry1(i)
  entry1?.set_text(i.to_s) unless i and i.start_with? '--'
end

#set_entry2(i) ⇒ Object

#

set_entry2

#


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 238

def set_entry2(i)
  entry2?.set_text(i.to_s) unless i and i.start_with? '--'
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/levensthein_distance/levensthein_distance.rb', line 181

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end