Class: Bioroebe::GUI::UniversalWidgets::FormatConverter

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

Overview

Bioroebe::GUI::UniversalWidgets::FormatConverter

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
'Format Converter'
WIDTH =
#

WIDTH

#
'75% or 2000px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 500px minimum'
FONT_LARGE =
#

FONT_LARGE

#
'Calibri 32'
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
USE_THIS_MONOFONT = 
MONOSPACED_FONT
SMALLER_FONT =
#

SMALLER_FONT

#
:hack_16
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16
TEXT1 =
#

TEXT1

#
'Available BLOSUM matrices:'

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) ⇒ FormatConverter

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 83

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::FormatConverter[]

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 395

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::FormatConverter.run

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 402

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::FormatConverter.new(i)
  )
  r.background_colour(:white)
  return r
end

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 124

def border_size?
  0
end

#calculated_weight?(i) ⇒ Boolean

#

calculated_weight?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 332

def calculated_weight?(i)
  this_file = Bioroebe.file_molecular_weight
  dataset = YAML.load_file(this_file)
  weight = 0
  if i.is_a?(String) and !i.empty?
    chars = i.chars.sort
    chars.each {|this_char|
      value = dataset[this_char]
      weight += value if value
    }
  end
  # ======================================================================= #
  # Must deduct water too.
  # ======================================================================= #
  weight -= (18.0 * (i.size - 1))
  return weight.round(2)
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 242

def connect_the_skeleton
  abort_on_exception

  vbox = create_vbox
  
  _ = left_aligned_label('Format Converter')
  _.make_bold
  vbox.minimal(_, 2)
  if first?
    @entry_input_sequence.set_text(first?.to_s)
  end
  hbox = create_hbox
  hbox.maximal(@entry_input_sequence, 1)
  event_box = gtk_event_box(image_file_open)
  event_box.hint = 'Click on this button in order to '\
    'open a local .FASTA file.'
  event_box.on_clicked {
    do_open_a_local_file
  }
  hbox.minimal(event_box,       1)
  vbox.add(hbox)
  @entry_input_sequence.on_enter {
    simulate_enter_click
  }
  hbox = create_hbox
  # ======================================================================= #
  # === button_do_convert
  # ======================================================================= #
  button_do_convert = button('_Do convert', self, :use_mnemonics) {
    :do_convert_the_file
  }
  button_do_convert.remove_background
  button_do_convert.bblack1
  button_do_convert.pad6px
  hbox.minimal(button_do_convert, 4)
  @combo_box = create_combo_box(
    %w( to_fasta )
  )
  @combo_box.bblack1
  @combo_box.first_is_active
  hbox.minimal(@combo_box, 4)
  vbox.minimal(hbox, 10)

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

  ::UniversalWidgets.set_main_window(window)
  ::Bioroebe.cd(::Bioroebe.log_dir?)
  menu
  window.use_this_font = font?
  window.show_all
  window.set_padding(padding?)
  window.set_border_size(border_size?)
  window.set_size_request(width?, height?)
  window.set_default_size(width?, height?)
  window.top_left
  run_main
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 219

def create_the_skeleton
  @text_buffer = create_text_buffer
  @text_view   = create_text_view(@text_buffer)
  create_user_input
end

#create_user_input ⇒ Object

#

create_user_input

#


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

def create_user_input
  # ======================================================================= #
  # === @entry_input_sequence
  # ======================================================================= #
  @entry_input_sequence = create_entry
  @entry_input_sequence.hint = 'This will denote the current file.'
  @entry_input_sequence.bblack1
  @entry_input_sequence.yellow_background
  @entry_input_sequence.pad5px
end

#do_convert_the_file ⇒ Object

#

do_convert_the_file

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 177

def do_convert_the_file
  _ = main_entry?.text?
  if _.empty?
    popup_over_this_widget(
      main_entry?,
      ' Please assign a file to work with first. '
    )
  else
    text = @combo_box.text?
    case text
    when 'to_fasta'
      result = Bioroebe.genbank_to_fasta(File.read(_))
    end
  end
end

#do_open_a_local_file(this_widget = @parent_widget) ⇒ Object

#

do_open_a_local_file

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 156

def do_open_a_local_file(
    this_widget = @parent_widget
  )
  require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
  widget = ::Gtk::SelectFile.new(this_widget) {{
    current_folder:         ::Bioroebe.log_dir?,
    additional_directories: ::Bioroebe.log_dir?
  }}
  this_file = widget.do_pick_file.text.to_s
  if File.exist?(this_file) and File.file?(this_file) # Ensure that it really is a file.
    dataset = File.read(this_file)
    set_main_entry(this_file.to_s)
    fill_with_this(dataset.to_s)
  end
  return this_file
end

#fill_with_this(i) ⇒ Object

#

fill_with_this

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 325

def fill_with_this(i)
  @text_buffer.set_text(i)
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/format_converter/format_converter.rb', line 145

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
'
  apply_the_CSS_rules
end

#main_entry? ⇒ Boolean

#

main_entry?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 388

def main_entry?
  @entry_input_sequence
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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

def main_font?
  USE_THIS_FONT
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 196

def menu(
    i = commandline_arguments?
  )
  if i.is_a? Array
    i.each {|entry| menu(entry) }
  else
    case i
    # ===================================================================== #
    # === gtk_aminoacid_composition --ubi
    # ===================================================================== #
    when /^-?-?ubiquitin$/i,
         /^-?-?ubi$/i
      set_main_entry(
        Bioroebe.return_ubiquitin_sequence
      )
      simulate_enter_click
    end
  end
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 117

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 98

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?
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 228

def run
  run_super
end

#set_main_entry(i) ⇒ Object Also known as: set_main_input_sequence

#

set_main_entry

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 374

def set_main_entry(i)
  @entry_input_sequence.set_text(i.to_s)
end

#set_main_input_sequence_and_evaluate_it(i) ⇒ Object

#

set_main_input_sequence_and_evaluate_it

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 381

def set_main_input_sequence_and_evaluate_it(i)
  simulate_enter_click(i)
end

#set_parent_widget(i) ⇒ Object

#

set_parent_widget

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 318

def set_parent_widget(i)
  @parent_widget = i
end

#simulate_enter_click(_ = @entry_input_sequence.text?) ⇒ Object

#

simulate_enter_click

#


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 353

def simulate_enter_click(
    _ = @entry_input_sequence.text?
  )
  _.upcase!
  _ = ::Bioroebe.filter_away_invalid_aminoacids(_)
  @entry_input_sequence.set_text(_)
  fill_the_table_data_with_this_sequence(_)
  @label_n_aminoacids.set_text(
    "This sequence has <b>#{_.size}</b> aminoacids."
  )
  @label_n_aminoacids.do_markify
  @label_molecular_weight.set_text(
    'The molecular weight is: <b>'+
    calculated_weight?(_).to_s+'</b> Dalton'
  )
  @label_molecular_weight.do_markify
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 138

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#smaller_font? ⇒ Boolean

#

smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/format_converter/format_converter.rb', line 235

def smaller_font?
  SMALLER_FONT
end