Class: Bioroebe::GUI::Gtk::Alignment

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

Overview

Bioroebe::GUI::Gtk::Alignment

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
'Alignment'
WIDTH =
#

WIDTH

#
'60%'
HEIGHT =
#

HEIGHT

#
'50%'
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_22
FONT_FOR_THE_ENTRIES =
#

FONT_FOR_THE_ENTRIES

The entries must use a mono-spaced font.

#
:hack_20

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) ⇒ Alignment

#

initialize

#

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

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

Class Method Details

.run(i = ARGV) ⇒ Object

#

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

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 300

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

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 106

def border_size?
  6
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 212

def connect_skeleton
  abort_on_exception
  minimal(return_the_first_row,                 5)
  minimal(@scrolled_window,          2)
  minimal(@button_do_analyse,        2)
  minimal(@entry_consensus_sequence, 2)
  minimal(@entry_numbers,            2)
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 245

def create_skeleton
  create_the_entries
  create_the_buttons
  create_the_text_buffer_and_the_text_view
  create_the_scrolled_window
end

#create_the_buttons ⇒ Object

#

create_the_buttons (buttons tag)

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 271

def create_the_buttons
  # ======================================================================= #
  # === @button_do_analyse
  # ======================================================================= #
  @button_do_analyse = bold_button('_Do analyse')
  @button_do_analyse.bblack1
  @button_do_analyse.on_hover(:lightblue)
  @button_do_analyse.hint = 'Click on this button to '\
    'analyse the given sequence. Make sure to use '\
    'newlines in order to split the sequence at hand.'
  @button_do_analyse.on_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."
      ).squeeze(' ')
    )
  }
end

#create_the_entries ⇒ Object

#

create_the_entries (entry tag, entries tag)

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 166

def create_the_entries
  # ======================================================================= #
  # === @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(
    'This entry will contain the consensus sequence, '\
    'derived from the above sequences.'
  )
  # ======================================================================= #
  # === @entry_numbers
  # ======================================================================= #
  @entry_numbers = gtk_entry
  @entry_numbers.use_this_font = FONT_FOR_THE_ENTRIES
  @entry_numbers.hint = 'This area may indicate the numbers for '\
                        'the alignment shown right above.'
end

#create_the_scrolled_window ⇒ Object

#

create_the_scrolled_window

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 113

def create_the_scrolled_window
  # ======================================================================= #
  # === @scrolled_window
  # ======================================================================= #
  @scrolled_window = gtk_scrolled_window(@text_view)
  @scrolled_window.width_height(300, 400)
  @scrolled_window.css_class('pad4px')
  @scrolled_window.bblack1
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/gtk3/alignment/alignment.rb', line 126

def create_the_text_buffer_and_the_text_view
  # ======================================================================= #
  # === @text_buffer
  # ======================================================================= #
  @text_buffer = gtk_text_buffer
  # ======================================================================= #
  # === @text_view
  # ======================================================================= #
  @text_view = gtk_text_view(@text_buffer)
end

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

#

do_analyse

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 147

def do_analyse(
    _ = @text_buffer.text?
  )
  if _ and !_.empty?
    _.strip!
    @alignment.use_this_as_input(_)
    consensus_sequence = @alignment.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_open_and_assign_a_local_file ⇒ Object

#

do_open_and_assign_a_local_file

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 314

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

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 99

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/gtk3/alignment/alignment.rb', line 191

def realign_the_numbers_showing_how_long_the_consensus_sequence_is
  @entry_numbers.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/gtk3/alignment/alignment.rb', line 80

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
  # ======================================================================= #
  # === @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/gtk3/alignment/alignment.rb', line 200

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

#return_the_first_row ⇒ Object

#

return_the_first_row

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 224

def return_the_first_row
  _ = gtk_hbox
  top_label = gtk_left_aligned_label(
    'Input the sequences that you wish to compare to one another'
  )
  top_label.center
  _.minimal(top_label)
  event_box = gtk_event_box(
    image_document_open
  )
  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)
  return _
end

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 264

def run
  create_skeleton_then_connect_skeleton
end

#text_view_widget? ⇒ Boolean

#

text_view_widget?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/alignment/alignment.rb', line 140

def text_view_widget?
  @text_view
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/gtk3/alignment/alignment.rb', line 255

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