Class: Bioroebe::GUI::UniversalWidgets::Alignment

Inherits:
UniversalWidgets::Base
  • Object
show all
Includes:
CommandlineArguments
Defined in:
lib/bioroebe/gui/universal_widgets/alignment/alignment.rb

Overview

Bioroebe::GUI::UniversalWidgets::Alignment

Constant Summary collapse

TITLE =
#

TITLE

#
'Alignment'
WIDTH =
#

WIDTH

#
'65% or 500px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 300px minimum'
USE_THIS_FONT =
#

USE_THIS_FONT

#
:hack_26
FONT_FOR_THE_ENTRIES =
#

FONT_FOR_THE_ENTRIES

The entries must use a mono-spaced font.

#
:hack_22
TEXT_INPUT_THE_SEQUENCES =
#

TEXT_INPUT_THE_SEQUENCES

#
'Input the sequences that you wish '\
'to compare to one another'
TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON =
#

TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON

#
"Click on this button to analyse the given sequence. Make sure "\
"to use <b>newlines</b> in order to split the sequence at hand."
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE =
#

TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE

This is the base-tooltip for the entry that retains our consensus sequence.

#
'This entry will contain the <b>consensus sequence</b>, '\
'derived from the above sequences.'
TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION =
#

TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION

#
"\n\nTake note that in the event that there is <b>an even number of "\
"input sequences</b>, the entries defined before will take precedence. "\
"So, for instance, if you have four sequences in total, where two are "\
"ATTA and the next two are ATTT, then the consensus sequence is "\
"currently assumed to be <b>ATTA</b>."

Constants included from ColoursForBase

ColoursForBase::ARRAY_HTML_COLOURS_IN_USE

Class Method Summary collapse

Instance Method Summary collapse

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) ⇒ Alignment

#

initialize

#


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

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::Alignment[]

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 502

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::Alignment.run

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 509

def self.run(
    i = ARGV
  )
  ::Gtk.gtk_runner_factory(
    ::Bioroebe::GUI::Gtk::Alignment.new(i)
  )
end

Instance Method Details

#alignment? ⇒ Boolean

#

alignment?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 478

def alignment?
  @alignment
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 222

def border_size?
  8
end

#button_convert? ⇒ Boolean

#

button_convert?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 278

def button_convert?
  @button_convert
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 520

def connect_the_skeleton
  abort_on_exception
  
  grid = default_grid
  grid.full_row(return_the_first_row)
  grid.full_row(@scrolled_window)
  grid.full_row(@entry_consensus_sequence)
  grid.full_row(@entry_numbers)
  grid.full_row(@button_do_analyse)
  grid.hcenter

  window = runner_widget(nil, width?, height?, title?)
  window << grid
  do_focus_on_the_textview
  ::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
  run_main
end

#create_the_buttons ⇒ Object

#

create_the_buttons (buttons tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 286

def create_the_buttons
  # ======================================================================= #
  # === @button_do_analyse
  # ======================================================================= #
  @button_do_analyse = bold_button('_Do analyse', self, :use_mnemonic) {
    :the_do_analyse_button_was_clicked
  }
  @button_do_analyse.clear_background
  @button_do_analyse.bblack1
  @button_do_analyse.on_hover(:lightblue)
  @button_do_analyse.hint = TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
end

#create_the_checkboxes ⇒ Object

#

create_the_checkboxes

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 266

def create_the_checkboxes
  # ======================================================================= #
  # === @checkbox1
  # ======================================================================= #
  @checkbox1 = create_checkbox
  @checkbox1.is_active
  @checkbox2 = create_checkbox
end

#create_the_consensus_sequence_entry ⇒ Object

#

create_the_consensus_sequence_entry

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 410

def create_the_consensus_sequence_entry
  # ======================================================================= #
  # === @entry_consensus_sequence
  # ======================================================================= #
  @entry_consensus_sequence = entry
  @entry_consensus_sequence.bblack1
  @entry_consensus_sequence.center
  @entry_consensus_sequence.use_this_font = FONT_FOR_THE_ENTRIES
  @entry_consensus_sequence.yellow_background
  update_the_hint_for_the_entry_consequences_sequence(
    TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE+
    TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
  )
end

#create_the_entries ⇒ Object

#

create_the_entries (entry tag, entries tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 164

def create_the_entries
  create_the_consensus_sequence_entry
  # ======================================================================= #
  # === @entry_numbers
  # ======================================================================= #
  @entry_numbers = create_entry
  @entry_numbers.bblack1
  @entry_numbers.use_this_font = FONT_FOR_THE_ENTRIES
  @entry_numbers.hint =
    'This area may indicate the numbers for '\
    'the alignment shown right above.'
  @entry_numbers.very_light_yellow_background
end

#create_the_scrolled_window ⇒ Object

#

create_the_scrolled_window

#


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

def create_the_scrolled_window
  # ======================================================================= #
  # === @scrolled_window
  # ======================================================================= #
  @scrolled_window = create_scrolled_window(@text_view)
  @scrolled_window.width_height(300, 400)
  @scrolled_window.pad4px
  @scrolled_window.bblack2
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 255

def create_the_skeleton
  create_the_checkboxes # Create the checkboxes first.
  create_the_entries
  create_the_buttons
  create_the_text_buffer_and_the_text_view
  create_the_scrolled_window
end

#create_the_text_buffer_and_the_text_view ⇒ Object

#

create_the_text_buffer_and_the_text_view

#


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

def create_the_text_buffer_and_the_text_view
  # ======================================================================= #
  # === @text_buffer
  # ======================================================================= #
  @text_buffer = create_text_buffer
  # ======================================================================= #
  # === @text_view
  # ======================================================================= #
  @text_view = create_text_view(@text_buffer)
end

#do_analyse(_ = text_buffer?.text?) ⇒ Object Also known as: do_analyse_again

#

do_analyse

This method will be called whenever the user hits the “Do analyse” button.

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 361

def do_analyse(
    _ = text_buffer?.text?
  )
  if _ and !_.empty?
    _.strip!
    alignment?.use_this_as_input(_)
    consensus_sequence = return_the_consensus_sequence
    @entry_consensus_sequence.set_text(consensus_sequence)
  else
    pop_up_widget(
      over_this_widget: text_view_widget?,
      text:             'Please assign a sequence first.'
    )
  end
end

#do_focus_on_the_textview ⇒ Object

#

do_focus_on_the_textview

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 549

def do_focus_on_the_textview
  textview?.do_focus
end

#do_open_and_assign_a_local_file ⇒ Object

#

do_open_and_assign_a_local_file

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 447

def do_open_and_assign_a_local_file
  open_local_file {{
    start_directory: log_dir?,
    additional_folders: [
      log_dir?,
      '/Depot/j/',
      '/Depot/jj/',
      '/Depot/jjj/',
      '/Depot/jjjj/'
    ]
  }}
  _ = main_file?
  if _ and File.exist?(_)
    dataset = File.read(_)
    @text_buffer.set_text(dataset)
    do_analyse_again
  end
end

#do_trigger_the_conversion(i = @entry1.text?, checkbox1 = @checkbox1) ⇒ Object Also known as: do_the_conversion

#

do_trigger_the_conversion (conversion tag)

This method is the one that will convert from the three-letter to the one-letter and vice versa.

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 305

def do_trigger_the_conversion(
    i         = @entry1.text?,
    checkbox1 = @checkbox1
  )
  i = i.to_s.dup.delete(' ')
  if checkbox1.active?
    new_result = Bioroebe.three_to_one(i).to_s
  else
    new_result = Bioroebe.one_to_three(i).to_s
  end
  if new_result and !new_result.empty?
    @entry2.set_text(new_result)
    @entry2.make_bold
  end
end

#entry_consensus_sequence? ⇒ Boolean

#

entry_consensus_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 428

def entry_consensus_sequence?
  @entry_consensus_sequence
end

#handle_CSS_rules ⇒ Object Also known as: handle_CSS

#

handle_CSS_rules (CSS tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 130

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  apply_the_CSS_rules
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 215

def padding?
  12
end

#realign_the_numbers_showing_how_long_the_consensus_sequence_is ⇒ Object

#

realign_the_numbers_showing_how_long_the_consensus_sequence_is

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 401

def realign_the_numbers_showing_how_long_the_consensus_sequence_is
  @entry_numbers.center if @entry_numbers.respond_to?(:center)
  n_characters = @entry_consensus_sequence.text?.size
  @entry_numbers.set_text(return_fill_up_to(n_characters))
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 110

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?
  reset_the_alignment_object
end

#reset_the_alignment_object ⇒ Object

#

reset_the_alignment_object

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 492

def reset_the_alignment_object
  # ======================================================================= #
  # === @alignment
  # ======================================================================= #
  @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
end

#return_fill_up_to(i) ⇒ Object

#

return_fill_up_to

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 435

def return_fill_up_to(i)
  _ = ''.dup
  i.times {|counter|
    counter = (counter+1) % 10
    _ << counter.to_s
  }
  return _
end

#return_the_checkbox_widget ⇒ Object

#

return_the_checkbox_widget

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 324

def return_the_checkbox_widget
  smaller_font = smaller_font?
  grid = default_grid
  text1 = text('3-to-1 conversion')
  text1.use_this_font(smaller_font)
  text1.hint = 'Convert the three letter code to the one letter code.'
pp text1
  grid.left(text1)
  grid.right(@checkbox1)
  text2 = text('1-to-3 conversion')
  text2.use_this_font(smaller_font)
  text2.hint = 'Convert the one letter code to the three letter code.'
  grid.left(text2)
  grid.right(@checkbox2)
  @checkbox1.on_toggled {
    if @checkbox1.active? == false
      @checkbox2.is_now_active
    else
      @checkbox2.is_now_inactive
    end
  }
  @checkbox2.on_toggled {
    if @checkbox2.active? == false
      @checkbox1.is_now_active
    else
      @checkbox1.is_now_inactive
    end
  }
  return grid
end

#return_the_consensus_sequence ⇒ Object

#

return_the_consensus_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 387

def return_the_consensus_sequence
  @alignment.consensus_sequence?
end

#return_the_first_row ⇒ Object

#

return_the_first_row

#


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

def return_the_first_row
  _ = create_hbox
  top_label = left_aligned_label(
    TEXT_INPUT_THE_SEQUENCES
  )
  top_label.make_selectable
  top_label.center
  _.minimal(top_label)
  use_this_image = image_document_open
  if use_this_image
    event_box = event_box(use_this_image)
    if event_box
      event_box.hint = 'Click on this icon to open a local file.'
      event_box.on_clicked {
        do_open_and_assign_a_local_file
      }
      _.pack_end(event_box)
    end
  end
  return _
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 380

def run
  run_super
end

#smaller_font? ⇒ Boolean

#

smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 229

def smaller_font?
  SMALLER_FONT
end

#text_buffer? ⇒ Boolean

#

text_buffer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 485

def text_buffer?
  @text_buffer
end

#text_view_widget? ⇒ Boolean

#

text_view_widget?

#

Returns:

  • (Boolean) 


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

def text_view_widget?
  @text_view
end

#textview? ⇒ Boolean

#

textview?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 195

def textview?
  @text_view
end

#the_do_analyse_button_was_clicked ⇒ Object

#

the_do_analyse_button_was_clicked

#


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

def the_do_analyse_button_was_clicked
  do_analyse
  realign_the_numbers_showing_how_long_the_consensus_sequence_is
  update_the_hint_for_the_entry_consequences_sequence(
    (
      "This entry will contain the consensus sequence, "\
      "derived from the above "+
      (@text_buffer.text?.count("\n")+1).to_s+" sequences.\n\nNote "\
      "that only the minimal length will be compared - "\
      "superfluous nucleotides will NOT be considered unless "\
      "they can be aligned to other sequences."+
      TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
    ).squeeze(' ')
  )
end

#update_the_hint_for_the_entry_consequences_sequence(i = '') ⇒ Object

#

update_the_hint_for_the_entry_consequences_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/alignment/alignment.rb', line 469

def update_the_hint_for_the_entry_consequences_sequence(
    i = ''
  )
  @entry_consensus_sequence.hint = i
end