Class: Bioroebe::GUI::UniversalWidgets::PrimerDesignWidget

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

Overview

Bioroebe::GUI::UniversalWidgets::PrimerDesignWidget

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
'Primer Design'
WIDTH =
#

WIDTH

#
'75% or 800px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 500px minimum'
PADDING_OF_THE_WHOLE_WIDGET =
#

PADDING_OF_THE_WHOLE_WIDGET

#
12
HUGE_FONT =
#

HUGE_FONT

#
:hack_25
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_HEADER =
#

USE_THIS_HEADER

#
['one-letter abbreviation', 'n times']
GENERATE_N_AMINOACIDS_BY_DEFAULT =
#

GENERATE_N_AMINOACIDS_BY_DEFAULT

#
15
COLOUR_FOR_NON_MATCHES =
#

COLOUR_FOR_NON_MATCHES

This is the colour that will be used for non-matching nucleotides.

#
:magenta

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) ⇒ PrimerDesignWidget

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 105

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::PrimerDesignWidget[]

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 594

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::PrimerDesignWidget.run

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 601

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::PrimerDesignWidget.new(i)
  )
  r.background_colour(:white)
  return r
end

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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

def border_size?
  2
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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

def connect_the_skeleton
  abort_on_exception
  
  outer_vbox = create_vbox
  outer_vbox.minimal(return_the_header_bar, 2)
  outer_vbox.minimal(return_the_main_label, 2)
  outer_vbox.minimal(@top_primer, 8)
  outer_vbox.minimal(hspacer)
  outer_vbox.minimal(@top_strand)
  @bottom_strand = bold_label("3'-#{@reverse_sequence}-5'")
  @bottom_strand.darkgreen
  outer_vbox.minimal(@bottom_strand)
  outer_vbox.minimal(hspacer)
  outer_vbox.minimal(@bottom_primer, 8)
  hbox = create_hbox
  hbox.minimal(text('Amplified area:'), 1)
  hbox.minimal(@amplified_area, 1)
  outer_vbox.minimal(hbox, 1)
  # ======================================================================= #
  # === The reverse primer will be added here
  # ======================================================================= #
  hbox = return_widget_containing_the_reverse_primer_information
  outer_vbox.minimal(hbox, 1)
  # ======================================================================= #
  # === The forward primer will be added here
  # ======================================================================= #
  hbox = return_widget_containing_the_forward_primer_information
  outer_vbox.minimal(hbox, 1)
  dragger = add_an_up_and_down_dragger(outer_vbox, @scrolled_window)

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

  ::UniversalWidgets.set_main_window(window)
  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?)
  sync_forward_and_reverse_primer
  Thread.new {
    sleep 0.001
    do_startup_related_actions
  }
  window.top_left
  run_main
end

#create_the_bottom_primer ⇒ Object

#

create_the_bottom_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 402

def create_the_bottom_primer
  # ======================================================================= #
  # === @bottom_primer
  # ======================================================================= #
  @bottom_primer = bold_label
  @bottom_primer.make_selectable
  @bottom_primer.tomato
  @bottom_primer.hint = 'This is the forward primer. A '\
    'match will be shown in green colour, whereas a '\
    'non-match will be shown in the '+
    COLOUR_FOR_NON_MATCHES.to_s+'-colour.'
end

#create_the_entries ⇒ Object

#

create_the_entries (entries tag, entry tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 332

def create_the_entries
  # ======================================================================= #
  # === @amplified_area
  # ======================================================================= #
  @amplified_area = create_entry
  @amplified_area.set_text('TACGTACG')
  @amplified_area.clear_background
  @amplified_area.lightblue_background
  @amplified_area.bblack1
  @amplified_area.pad5px
  # ======================================================================= #
  # === @reverse_primer
  # ======================================================================= #
  @reverse_primer = create_entry
  @reverse_primer.yellow_background
  @reverse_primer.bblack1
  @reverse_primer.width_height(250, 50)
  @reverse_primer.set_text(@reverse_sequence.reverse[0,3])
  @reverse_primer.hint = ''
  @reverse_primer.on_changed {
    @reverse_primer.set_text(@reverse_primer.text?.upcase)
    sync_the_reverse_primer
    do_calculate_GC_content_for_the_reverse_primer
  }
  # ======================================================================= #
  # === @forward_primer
  # ======================================================================= #
  @forward_primer = create_entry
  @forward_primer.yellow_background
  @forward_primer.bblack1
  @forward_primer.width_height(250, 50)
  @forward_primer.set_text('ATG')
  @forward_primer.on_changed {
    @forward_primer.set_text(@forward_primer.text?.upcase)
    sync_the_forward_primer
    do_calculate_GC_content_for_the_forward_primer
  }
  @forward_primer.hint = "The forward primer is the sequence "\
    "corresponding to the sense strand (5'→3'). It appears "\
    "on the bottom side of the above text."
end

#create_the_header_bar ⇒ Object

#

create_the_header_bar

#


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

def create_the_header_bar
  @header_bar = default_header_bar
  @header_bar.pad8px
  @header_bar.bblack1
  event_box = create_event_box(image_information)
  event_box.hint = 'Click on this image to show some information '\
                   'about <b>primer design</b> in a PCR.'
  event_box.on_clicked {
    do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR
  }
  @header_bar.add_left(event_box)
end

#create_the_scrolled_window ⇒ Object

#

create_the_scrolled_window (scrolled tag)

#


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

def create_the_scrolled_window
  @text_buffer = create_text_buffer
  @text_view = create_text_view(@text_buffer)
  # ======================================================================= #
  # === @scrolled_window
  # ======================================================================= #
  @scrolled_window = create_scrolled_window(@text_view) { :always }
  @scrolled_window.bblack1
  @scrolled_window.pad8px
  @scrolled_window.width_height(500, 400)
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 193

def create_the_skeleton
  create_the_entries
  create_the_header_bar
  create_the_scrolled_window
  create_the_top_primer
  create_the_top_strand
  create_the_bottom_primer
end

#create_the_top_primer ⇒ Object

#

create_the_top_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 377

def create_the_top_primer
  # ======================================================================= #
  # === @top_primer
  # ======================================================================= #
  @top_primer = bold_label
  @top_primer.make_selectable
  @top_primer.tomato
  @top_primer.hint =
    'This is the reverse primer. A '\
    'match will be shown in green colour, whereas a '\
    'non-match will be shown in the '+
    COLOUR_FOR_NON_MATCHES.to_s+'-colour.'
end

#create_the_top_strand ⇒ Object

#

create_the_top_strand

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 230

def create_the_top_strand
  @top_strand = bold_label("5'-#{@forward_sequence}-3'")
  @top_strand.darkblue
end

#do_calculate_the_GC_content_for_the_forward_primer ⇒ Object Also known as: do_calculate_GC_content_for_the_forward_primer

#

do_calculate_the_GC_content_for_the_forward_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 626

def do_calculate_the_GC_content_for_the_forward_primer
  _ = ::Bioroebe.gc_content_of_this_sequence(
    @forward_primer.text?.to_s, 1 # The second number is for how much to round.
  )
  _ = 0 if _ == 'NaN'
  @text_GC_content_for_the_forward_primer_as_percentage.set_text("#{_}%")
end

#do_calculate_the_GC_content_for_the_reverse_primer ⇒ Object Also known as: do_calculate_GC_content_for_the_reverse_primer

#

do_calculate_the_GC_content_for_the_reverse_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 615

def do_calculate_the_GC_content_for_the_reverse_primer
  _ = ::Bioroebe.gc_content_of_this_sequence(
    @reverse_primer.text?.to_s, 1 # The second number is for how much to round.
  )
  _ = 0 if _ == 'NaN'
  @text_GC_content_for_the_reverse_primer_as_percentage.set_text("#{_}%")
end

#do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR ⇒ Object

#

do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 434

def do_pop_up_the_widget_containing_information_about_primer_design_in_a_PCR
  vbox = create_vbox
  # ======================================================================= #
  # Style this vbox a bit:
  # ======================================================================= #
  outer_vbox = create_vbox
  outer_vbox.set_border_width(8)
  outer_vbox.pad8px
  outer_vbox.bblack1
  vbox.pad5px
  vbox.use_this_font = :hack_18
  vbox.add_hspacer
  _ = left_aligned_text(
    'Some advice on primer design'
  )
  _.use_this_font = :hack_20
  vbox.minimal(_, 10)
  vbox.add_hspacer
  vbox.add(
    left_aligned_text(
      ' - use a moderate G+C content'
    )
  )
  vbox.add(
    left_aligned_text(
      ' - binding region should be 17-27 bp'
    )
  )
  vbox.add(
    left_aligned_text(
      " - binding region Tm’s in the range of 50 to 65°C"
    )
  )
  vbox.add(
    left_aligned_text(
      ' - avoid repetitive poly-N regions'
    )
  )
  vbox.add(
    left_aligned_text(
      ' - avoid secondary structure (hairpins, '\
      'self dimerization or primer dimer)'
    )
  )
  vbox.add(
    left_aligned_text(
      " - primer pairs should have similar Tm's (±4°C)"
    )
  )
  vbox.add_hspacer
  outer_vbox.maximal(vbox, 2)
  pop_up_widget(
    over_this_widget: main_label?,
    custom_widget:    outer_vbox
  ).popup
end

#do_startup_related_actions ⇒ Object

#
#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 322

def do_startup_related_actions
  print ' '
  @top_primer.deselect
  do_calculate_the_GC_content_for_the_reverse_primer
  do_calculate_the_GC_content_for_the_forward_primer
end

#establish_the_forward_and_reverse_sequence ⇒ Object

#

establish_the_forward_and_reverse_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 140

def establish_the_forward_and_reverse_sequence
  # ======================================================================= #
  # === @forward_sequence
  # ======================================================================= #
  @forward_sequence = 'ATGAGGTTTGCAGCG'
  # ======================================================================= #
  # === @reverse_sequence
  # ======================================================================= #
  @reverse_sequence = 'TACTCCAAACGTCGC'
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/primer_design_widget/primer_design_widget.rb', line 182

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
'
  apply_the_CSS_rules
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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

def main_font?
  USE_THIS_FONT
end

#main_label? ⇒ Boolean

#

main_label?

#

Returns:

  • (Boolean) 


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

def main_label?
  @main_label
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 154

def padding?
  PADDING_OF_THE_WHOLE_WIDGET
end

#remove_ends(i = "3'-TACGTACGTACGTACG-5'") ⇒ Object

#

remove_ends

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 637

def remove_ends(
    i = "3'-TACGTACGTACGTACG-5'"
  )
  i = i.dup
  i.sub!(/3'-/,'')
  i.sub!(/-5'/,'')
  i.sub!(/5'-/,'')
  i.sub!(/'3-/,'')
  i.sub!(/-'5/,'')
  return i
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 120

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?
  establish_the_forward_and_reverse_sequence
end

#return_the_header_bar ⇒ Object

#

return_the_header_bar

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 223

def return_the_header_bar
  return @header_bar
end

#return_the_main_label ⇒ Object

#

return_the_main_label

#


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

def return_the_main_label
  @main_label = left_aligned_label(TITLE)
  @main_label.make_bold
  @main_label.use_this_font = HUGE_FONT
  @main_label.make_selectable
  return @main_label
end

#return_widget_containing_the_forward_primer_information ⇒ Object

#

return_widget_containing_the_forward_primer_information

#


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

def return_widget_containing_the_forward_primer_information
  hbox = create_hbox
  hbox.minimal(bold_text("Forward primer: 5'-"), 1)
  hbox.minimal(@forward_primer, 1)
  hbox.minimal(bold_text("-3'",1))
  button1 = button('←')
  button1.hint = 'Remove the last nucleotide from the primer.'
  button1.bblack1
  button1.on_clicked {
    @forward_primer.try_to_remove_the_last_character
  }
  hbox.minimal(button1)
  text_showing_the_GC_content = left_aligned_text(' GC content:')
  text_showing_the_GC_content.use_this_font = smaller_font?
  text_showing_the_GC_content.make_bold
  hbox.minimal(text_showing_the_GC_content, 5)
  @text_GC_content_for_the_forward_primer_as_percentage = left_aligned_text
  @text_GC_content_for_the_forward_primer_as_percentage.use_this_font = smaller_font?
  @text_GC_content_for_the_forward_primer_as_percentage.make_bold
  hbox.minimal(@text_GC_content_for_the_forward_primer_as_percentage, 5)
  return hbox
end

#return_widget_containing_the_reverse_primer_information ⇒ Object

#

return_widget_containing_the_reverse_primer_information

This is the widget that contains the various smaller widgets necessary for the “Reverse primer:” info, close to the bottom of this widget.

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 256

def return_widget_containing_the_reverse_primer_information
  hbox = create_hbox
  hbox.minimal(bold_text("Reverse primer: 5'-"),1)
  hbox.minimal(@reverse_primer,1)
  hbox.minimal(bold_text("-3'",1))
  button2 = button('←')
  button2.hint = 'Remove the last nucleotide from the primer.'
  button2.bblack1
  button2.on_clicked {
    @reverse_primer.try_to_remove_the_last_character
  }
  hbox.minimal(button2)
  text_showing_the_GC_content = left_aligned_text(' GC content:')
  text_showing_the_GC_content.use_this_font = smaller_font?
  text_showing_the_GC_content.make_bold
  hbox.minimal(text_showing_the_GC_content, 5)
  @text_GC_content_for_the_reverse_primer_as_percentage = left_aligned_text
  @text_GC_content_for_the_reverse_primer_as_percentage.use_this_font = smaller_font?
  @text_GC_content_for_the_reverse_primer_as_percentage.make_bold
  hbox.minimal(@text_GC_content_for_the_reverse_primer_as_percentage, 5)
  return hbox
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 205

def run
  run_super
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#smaller_font? ⇒ Boolean

#

smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 315

def smaller_font?
  SMALLER_FONT
end

#sync_forward_and_reverse_primer ⇒ Object

#

sync_forward_and_reverse_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 394

def sync_forward_and_reverse_primer
  sync_forward_primer
  sync_reverse_primer
end

#sync_forward_primer ⇒ Object Also known as: sync_the_forward_primer

#

sync_forward_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 494

def sync_forward_primer
  _ = @forward_primer.text?
  longer_nucleotide_sequence = remove_ends(@bottom_strand.text?)
  array = ["      5'-", :tomato]
  _.chars.each_with_index {|char, index|
    if char == Bioroebe.should_match_to?(longer_nucleotide_sequence[index])
      # This is a match.
      array << [char, :darkgreen]
    else
      # This is NOT a match.
      array << [char, COLOUR_FOR_NON_MATCHES]
    end
    array.flatten!
  }
  array << ["-3'→".ljust(@forward_sequence.size+(9-_.size)), :tomato]
  array.flatten!
  @bottom_primer.simple_markup(array)
end

#sync_reverse_primer ⇒ Object Also known as: sync_the_reverse_primer

#

sync_reverse_primer

#


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# File 'lib/bioroebe/gui/universal_widgets/primer_design_widget/primer_design_widget.rb', line 516

def sync_reverse_primer
  _ = @reverse_primer.text?
  longer_nucleotide_sequence = remove_ends(@top_strand.text?.reverse)
  @top_primer.set_text(
    _.rjust(@forward_sequence.size+6)
  )
  array = ["←3'-".rjust(33), :tomato]
  _.chars.reverse.each_with_index {|char, index|
    if char == Bioroebe.should_match_to?(longer_nucleotide_sequence[index])
      # This is a match.
      array << [char, :darkgreen]
    else
      # This is NOT a match.
      array << [char, COLOUR_FOR_NON_MATCHES]
    end
    array.flatten!
  }
  array << ["-5'".ljust(@forward_sequence.size+6), :tomato]
  array.flatten!
  @top_primer.simple_markup(array)
end