Class: Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes

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

Overview

Bioroebe::GUI::UniversalWidgets::RestrictionEnzymes

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this small widget.

#
'Restriction Enzymes'
WIDTH =
#

WIDTH

#
'65% or 600px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 400px 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
FILE_RESTRICTION_ENZYMES =
#

FILE_RESTRICTION_ENZYMES

#
::Bioroebe.restriction_enzymes_file?

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) ⇒ RestrictionEnzymes

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 80

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::RestrictionEnzymes[]

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 370

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::RestrictionEnzymes.run

#


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

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::RestrictionEnzymes.new(i)
  )
  r.modify_background(:normal, :mintcream)
  r.set_border_width(4)
  r.add_shortcut(1, 'focus_entry(1)', :alt)
  r.add_shortcut(2, 'focus_entry(2)', :alt)
  r.add_shortcut(3, 'focus_entry(3)', :alt)
  r.add_shortcut(4, 'focus_entry(4)', :alt)
  r.background_colour :whitesmoke
  return r
end

Instance Method Details

#add_status_message(i) ⇒ Object

#

add_status_message

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 303

def add_status_message(i)
  @statusbar.set_text(i)
  @statusbar.do_markify
  return @statusbar
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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

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/restriction_enzymes/restriction_enzymes.rb', line 328

def connect_the_skeleton
  abort_on_exception

  vbox = create_vbox
  
  text1 = selectable_text('<b>'+@yaml.keys.size.to_s+'</b> restriction enzymes '\
          'are registered.')
  vbox.minimal(text1, 1)
  hbox1 = create_hbox
  hbox1.minimal(@combo_box,       5)
  hbox1.minimal(@entry_selection, 5)
  vbox.minimal(hbox1, 1)
  vbox.minimal(return_widget_in_the_second_row_starting_with_a_gtk_entry_widget, 1)
  vbox.minimal(@statusbar, 1)
  # ======================================================================= #
  # Show a simple status-message on the bottom of this widget.
  # ======================================================================= #
  add_status_message('')

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

  ::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?)
  window.top_left
  Thread.new {
    sleep 0.0001
    @entry_search.do_focus
  }
  run_main
end

#create_status_bar ⇒ Object

#

create_status_bar

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 197

def create_status_bar
  # ======================================================================= #
  # === @statusbar
  # ======================================================================= #
  @statusbar = create_label
  @statusbar.align_left
end

#create_the_combo_box ⇒ Object

#

create_the_combo_box

rf gtk combobox

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 273

def create_the_combo_box
  @combo_box = create_combo_box(:strings_only)
  @combo_box.bblack1
  @combo_box.use_this_font(:hack_21)
  @yaml.each {|name_of_the_restriction_enzyme, cuts_at_this_location|
    # ===================================================================== #
    # The entries will be like this:
    #   ["PshBI", "ATTAAT   2"]
    # ===================================================================== #
    @hash_restriction_enzymes[name_of_the_restriction_enzyme] =
      cuts_at_this_location
    _ = "#{name_of_the_restriction_enzyme.ljust(10,' ')} → #{cuts_at_this_location}"
    @combo_box.append_text(_)
  }
  @combo_box.on_changed {
    if @combo_box.active_iter
      _ = @combo_box.active_iter[0]
      @entry_selection.set_text(_)
      if _.include? '→'
        _ = _.split('→').last.strip.split(' ').first.to_s
      end
      @entry_showing_only_the_sequence_that_is_to_be_cut.set_text(_)
    end
  }
  @combo_box.active = 0
end

#create_the_entries ⇒ Object

#

create_the_entries (entries tag, entry tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 167

def create_the_entries
  # ======================================================================= #
  # === @entry_showing_only_the_sequence_that_is_to_be_cut
  # ======================================================================= #
  @entry_showing_only_the_sequence_that_is_to_be_cut = create_entry
  @entry_showing_only_the_sequence_that_is_to_be_cut.width_height(400, 42)
  @entry_showing_only_the_sequence_that_is_to_be_cut.clear_background
  @entry_showing_only_the_sequence_that_is_to_be_cut.make_bold
  @entry_showing_only_the_sequence_that_is_to_be_cut.align_to_the_center
  @entry_showing_only_the_sequence_that_is_to_be_cut.bblack2
  @entry_showing_only_the_sequence_that_is_to_be_cut.very_light_yellowish_background
  @entry_showing_only_the_sequence_that_is_to_be_cut.hint = 
    'This entry shows at which sequence the selected restriction '\
    'enzyme will cut.'
  # ======================================================================= #
  # === @entry_selection
  # ======================================================================= #
  @entry_selection = create_entry
  @entry_selection.clear_background
  @entry_selection.bblack1
  @entry_selection.width_height(540, 42)
  @entry_selection.on_button_press_event { |widget, event|
    @entry_selection.set_focus(true)
    # @entry_selection.select_everything
  }
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 312

def create_the_skeleton
  create_the_entries
  create_the_combo_box
  create_status_bar
end

#do_popup_with_this_message(i = 'No restriction enzyme is known with this name.') ⇒ Object

#

do_popup_with_this_message

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 262

def do_popup_with_this_message(
    i = 'No restriction enzyme is known with this name.'
  )
  return_popover(i, @entry_search, 5).popup
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/restriction_enzymes/restriction_enzymes.rb', line 155

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

  '
  apply_the_CSS_rules
end

#load_yaml_file(i = FILE_RESTRICTION_ENZYMES) ⇒ Object

#

load_yaml_file

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 208

def load_yaml_file(
    i = FILE_RESTRICTION_ENZYMES
  )
  @yaml = YAML.load_file(i)
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 127

def padding?
  8
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 95

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?
  # ======================================================================= #
  # === @hash_restriction_enzymes
  # ======================================================================= #
  @hash_restriction_enzymes = {}
  # ======================================================================= #
  # Try to load the restriction enzymes next.
  # ======================================================================= #
  _ = FILE_RESTRICTION_ENZYMES
  if File.exist? _
    load_yaml_file
  else
    e "No file at #{_} was found."
  end
end

#return_widget_in_the_second_row_starting_with_a_gtk_entry_widget ⇒ Object

#

return_widget_in_the_second_row_starting_with_a_gtk_entry_widget

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 217

def return_widget_in_the_second_row_starting_with_a_gtk_entry_widget
  hbox = create_hbox
  # ======================================================================= #
  # === @entry_search
  # ======================================================================= #
  @entry_search = create_search_entry
  @entry_search.clear_background
  @entry_search.bblack1
  @entry_search.on_enter {
    try_to_pick_this_restriction_enzyme(@entry_search.text?)
  }
  hbox.minimal(@entry_search,                                      5)
  hbox.minimal(@entry_showing_only_the_sequence_that_is_to_be_cut, 5)
  return hbox
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 321

def run
  run_super
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/restriction_enzymes/restriction_enzymes.rb', line 148

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#try_to_pick_this_restriction_enzyme(i = @entry_search.text?) ⇒ Object

#

try_to_pick_this_restriction_enzyme

#


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

def try_to_pick_this_restriction_enzyme(
    i = @entry_search.text?
  )
  i.strip!
  # ======================================================================= #
  # Next compare the text to the available restriction enzymes. Right
  # now this is limited to 100% matches, but we may extend this at
  # a later time to have partial matches as well.
  # ======================================================================= #
  if @hash_restriction_enzymes.has_key? i
    use_this_index = @hash_restriction_enzymes.find_index {|key, value | key == i }
    @combo_box.set_active(use_this_index)
  else
    # ===================================================================== #
    # The colour is red, for the emphasis-part.
    # ===================================================================== #
    do_popup_with_this_message(
      'No restriction enzyme is known with this '\
      'name: `<span weight="600" foreground="#de6b57">'+i.to_s+'</span>`'
    )
  end
end