Class: Bioroebe::GUI::Gtk::RestrictionEnzymes

Inherits:
Gtk::Box
  • Object
show all
Includes:
Bioroebe::GUI, Bioroebe::GUI::Gtk, Gtk::BaseModule
Defined in:
lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb

Overview

Bioroebe::GUI::Gtk::RestrictionEnzymes

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
'Restriction Enzymes'
FILE_RESTRICTION_ENZYMES =
#

FILE_RESTRICTION_ENZYMES

#
::Bioroebe.restriction_enzymes_file?
WIDTH =
#

WIDTH

#
940
HEIGHT =
#

HEIGHT

#
'20% or minimum 200px'
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_21

Constants included from Bioroebe::GUI

ARRAY_ALL_GTK_WIDGETS, FONT_SIZE, OLD_VERBOSE_VALUE, USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS

Class Method Summary collapse

Instance Method Summary collapse

Methods included from Bioroebe::GUI

#disable_warnings, #enable_warnings, #log_dir?

Constructor Details

#initialize(commandline_arguments = ARGV, run_already = true) ⇒ RestrictionEnzymes

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 65

def initialize(
    commandline_arguments = ARGV,
    run_already           = true
  )
  super(:vertical)
  reset
  set_commandline_arguments(
    commandline_arguments
  )
  modify_background(:normal, :white)
  run if run_already
end

Class Method Details

.run(i = ARGV) ⇒ Object

#

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

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 287

def self.run(
    i = ARGV
  )
  require 'gtk_paradise/run'
  _ = ::Bioroebe::GUI::Gtk::RestrictionEnzymes.new(i)
  r = ::Gtk.run
  r << _
  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
  r.infer_the_size
  r.top_left_then_run
end

Instance Method Details

#add_status_message(i) ⇒ Object

#

add_status_message

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 164

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

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

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

def border_size?
  0
end

#connect_skeleton ⇒ Object

#

connect_skeleton (skeleton tag)

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 308

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

#create_combo_box ⇒ Object

#

create_combo_box

rf gtk combobox

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 134

def create_combo_box
  @combo_box = gtk_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_entries ⇒ Object

#

create_entries (entries tag, entry tag)

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 246

def create_entries
  # ======================================================================= #
  # === @entry_showing_only_the_sequence_that_is_to_be_cut
  # ======================================================================= #
  @entry_showing_only_the_sequence_that_is_to_be_cut = gtk_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 = gtk_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_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 226

def create_skeleton
  create_entries
  create_combo_box
  create_status_bar
end

#create_status_bar ⇒ Object

#

create_status_bar

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 235

def create_status_bar
  # ======================================================================= #
  # === @statusbar
  # ======================================================================= #
  @statusbar = gtk_label
  @statusbar.align_left
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/gtk3/restriction_enzymes/restriction_enzymes.rb', line 217

def do_popup_with_this_message(
    i = 'No restriction enzyme is known with this name.'
  )
  return_popover(i, @entry_search, 5).popup
end

#load_yaml_file(i = FILE_RESTRICTION_ENZYMES) ⇒ Object

#

load_yaml_file

#

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

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

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 109

def padding?
  6
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb', line 81

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 
  infer_the_size_automatically
  # ======================================================================= #
  # === @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/gtk3/restriction_enzymes/restriction_enzymes.rb', line 172

def return_widget_in_the_second_row_starting_with_a_gtk_entry_widget
  hbox = gtk_hbox
  # ======================================================================= #
  # === @entry_search
  # ======================================================================= #
  @entry_search = gtk_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/gtk3/restriction_enzymes/restriction_enzymes.rb', line 276

def run
  super()
  Thread.new {
    sleep 0.0001
    @entry_search.do_focus
  }
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/gtk3/restriction_enzymes/restriction_enzymes.rb', line 191

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