Class: Bioroebe::GUI::UniversalWidgets::ShowCodonUsage

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

Overview

Bioroebe::GUI::UniversalWidgets::ShowCodonUsage

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this small widget.

#
'Show Codon Usage'
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
TEST_SEQUENCE =
#

TEST_SEQUENCE

#
'AGACGTACGTACGTCAGTCAGTACGTACTGATCGTAGCTAGCTACGTGACC'

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) ⇒ ShowCodonUsage

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 77

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::ShowCodonUsage[]

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 372

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::ShowCodonUsage.run

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 379

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::ShowCodonUsage.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/show_codon_usage/show_codon_usage.rb', line 125

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/show_codon_usage/show_codon_usage.rb', line 329

def connect_the_skeleton
  abort_on_exception

  vbox = create_vbox

  handle_the_commandline_arguments
  vbox.minimal(@entry1)
  update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence
  vbox.minimal(@label_showing_n_nucleotides)
  vbox.minimal(hspacer)
  create_box_top_five_codons
  @box_top_five_codons.minimal(@label_top_five_codons, 10)
  draggable_pane = gtk_drag_top_to_bottom(
    @scrolled_window,
    @box_top_five_codons
  )
  vbox.maximal(draggable_pane)

  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?)
  handle_the_commandline_arguments # This must come after the GUI skeleton was created.
  Thread.new {
    sleep 0.02
    do_the_conversion_then_update_the_label_as_well
    @entry1.deselect
  }
  window.top_left
  run_main
end

#create_box_top_five_codons ⇒ Object

#

create_box_top_five_codons

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 131

def create_box_top_five_codons
  @box_top_five_codons = create_vbox
  @box_top_five_codons.set_font(:hack_20)
end

#create_the_label_showing_n_nucleotides ⇒ Object

#

create_the_label_showing_n_nucleotides

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 146

def create_the_label_showing_n_nucleotides
  @label_showing_n_nucleotides = label
  @label_showing_n_nucleotides.set_font('Bitstream Vera Sans 22')
end

#create_the_label_top_five_codons ⇒ Object

#

create_the_label_top_five_codons

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 139

def create_the_label_top_five_codons
  @label_top_five_codons = label
end

#create_the_main_entry ⇒ Object

#

create_the_main_entry (entry tag)

#


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

def create_the_main_entry
  # ======================================================================= #
  # === @entry1
  # ======================================================================= #
  @entry1 = create_entry
  @entry1.set_text(@use_this_as_the_input_sequence)
  @entry1.set_font(:hack_20)
  @entry1.hint =
    "This entry should contain the nucleotide sequence that "\
    "the user wants to analyse. \n\nAs soon as the user has "\
    "finished the sequence, the '<b>enter</b>' key can be used "\
    "to analyse the sequence."
  @entry1.on_enter {
    do_the_conversion_then_update_the_label_as_well
  } if @entry1.respond_to? :on_enter
end

#create_the_scrolled_window ⇒ Object

#

create_the_scrolled_window (scrolled tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 289

def create_the_scrolled_window
  # ======================================================================= #
  # === @scrolled_window
  # ======================================================================= #
  @scrolled_window = create_scrolled_window(@text_view) { :only_top_and_bottom_scrollbar }
  @scrolled_window.set_font(:hack_20)
  @scrolled_window.read_only
  @scrolled_window.pad8px
  @scrolled_window.set_border_width(5)
  @scrolled_window.set_size_request(550, 300)
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 304

def create_the_skeleton
  create_the_label_showing_n_nucleotides
  create_the_main_entry
  create_the_label_top_five_codons
  create_the_text_view # Must be created before the scrolled window.
  create_the_scrolled_window
end

#create_the_text_view ⇒ Object

#

create_the_text_view

#


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

def create_the_text_view
  @text_view = create_text_view
end

#do_the_conversion(i = @entry1.text?) ⇒ Object

#

do_the_conversion

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 210

def do_the_conversion(
    i = @entry1.text?
  )
  # ======================================================================= #
  # First, we remove any numbers from the given input at hand:
  # ======================================================================= #
  shortened_sequence = ::Bioroebe.remove_numbers_from(i)
  unless i == shortened_sequence
    i = shortened_sequence
    @entry1.set_text(i)
  end
  hash = Bioroebe::ShowCodonUsage.new(i) { :be_quiet }.result?
  _ = ''.dup     
  hash.each_pair {|key, value|
    _ << "#{key}: #{value}\n"
  }
  text_for_the_label = "The <b>top 5 codons</b> are:\n\n".dup
  keys = hash.keys[0 .. 4] # Grab the first 5 entries.
  hash.each_pair {|key, value|
    if keys.include? key
      if use_gtk3?
        text_for_the_label << '<b>'+key.to_s+'</b>: '+value.to_s+"\n"
      else
        text_for_the_label << key.to_s+': '+value.to_s+"\n"
      end
    end
  }
  @label_top_five_codons.set_text(
    text_for_the_label
  )
  @label_top_five_codons.make_selectable
  @label_top_five_codons.do_markify # Apply any markup rules here.
  @text_view.set_text(_.strip)
end

#do_the_conversion_then_update_the_label_as_well ⇒ Object

#

do_the_conversion_then_update_the_label_as_well

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 202

def do_the_conversion_then_update_the_label_as_well
  do_the_conversion
  update_the_label_as_well
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/show_codon_usage/show_codon_usage.rb', line 277

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

  '
  apply_the_CSS_rules
end

#handle_the_commandline_arguments(i = commandline_arguments? ) ⇒ Object

#

handle_the_commandline_arguments

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 248

def handle_the_commandline_arguments(
    i = commandline_arguments?
  )
  i.each {|entry|
    if File.file? entry
      @use_this_as_the_input_sequence = File.read(entry).
                                        strip.delete("\n").delete(' ')
      sync_the_input_sequence_onto_the_main_entry
    end
  }
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 263

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 118

def padding?
  8
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 92

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?
  # ======================================================================= #
  # === @use_this_as_the_input_sequence
  #
  # Assign a dummy-sequence for startup. This can be changed via the
  # commandline-input.
  # ======================================================================= #
  @use_this_as_the_input_sequence = TEST_SEQUENCE
end

#run ⇒ Object

#

run (run tag)

#


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

def run
  run_super
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/show_codon_usage/show_codon_usage.rb', line 270

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#sync_the_input_sequence_onto_the_main_entry(i = @use_this_as_the_input_sequence) ⇒ Object

#

sync_the_input_sequence_onto_the_main_entry

#


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

def sync_the_input_sequence_onto_the_main_entry(
    i = @use_this_as_the_input_sequence
  )
  if i
    @entry1.set_text(i)
    update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence(i)
    do_the_conversion_then_update_the_label_as_well unless i.empty?
  end
end

#update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence(i = @entry1.text?.size.to_s) ⇒ Object Also known as: update_the_label_as_well

#

update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence

#


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

def update_the_main_label_denoting_how_many_nucleotides_can_be_found_in_the_main_sequence(
    i = @entry1.text?.size.to_s
  )
  if use_gtk3?
    _ = "n nucleotides: <b>#{i}</b>"
  else
    _ = "n nucleotides: #{i}"
  end
  @label_showing_n_nucleotides.set_text(_)
  @label_showing_n_nucleotides.do_markify
end