Class: Bioroebe::GUI::UniversalWidgets::AminoacidComposition

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

Overview

Bioroebe::GUI::UniversalWidgets::AminoacidComposition

Constant Summary collapse

TITLE =
#

TITLE

#
'Aminoacid Composition'
WIDTH =
#

WIDTH

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

HEIGHT

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

USE_THIS_FONT

#
:hack_26
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16
USE_THIS_TITLE_FOR_THE_MAIN_BUTTON =
#

USE_THIS_TITLE_FOR_THE_MAIN_BUTTON

#
'_Determine the DNA sequence'
FONT_FOR_THE_ENTRIES =
#

FONT_FOR_THE_ENTRIES

The entries must use a mono-spaced font.

#
:hack_22
FILE_MOLECULAR_WEIGHT =
#

FILE_MOLECULAR_WEIGHT

#
Bioroebe.file_molecular_weight

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) ⇒ AminoacidComposition

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 67

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::AminoacidComposition[]

#


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

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::AminoacidComposition.run

#


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

def self.run(
    i = ARGV
  )
  ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::ProteinToDNA.new(i)
  )
end

Instance Method Details

#aminoacid_sequence? ⇒ Boolean

#

aminoacid_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 302

def aminoacid_sequence?
  left_buffer?.to_s
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 237

def border_size?
  0
end

#calculated_weight?(i) ⇒ Boolean

#

calculated_weight?

This method will calculate the weight.

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 112

def calculated_weight?(i)
  dataset = YAML.load_file(FILE_MOLECULAR_WEIGHT)
  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/protein_to_DNA/protein_to_DNA.rb', line 360

def connect_the_skeleton
  abort_on_exception
  @main_vbox.maximal(top_hbox?, 4)
  @main_vbox.maximal(@middle_bar)
  button_box = button_box(
    @dataset[:backtrack_button],
    @dataset[:quit_button]
  )
  button_box.vertical_layout
  @main_vbox.minimal(button_box)

  window = runner_widget(nil, width?, height?, title?)
  window << @main_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?)
  window.top_left
  run_main
end

#create_buttons ⇒ Object

#

create_buttons (buttons tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 244

def create_buttons
  backtrack_button = bold_button(
    USE_THIS_TITLE_FOR_THE_MAIN_BUTTON, self, :use_mnemonic
  ) {
    :do_determine_the_backtrack_sequence
  }
  backtrack_button.set_name('button1')
  backtrack_button.do_use_underline
  backtrack_button.hint = 
    "On the <b>left hand side</b>, you should input the "\
    "Aminoacid sequence.\n\n"\
    "On the <b>right hand side</b>, a possible DNA "\
    "sequence for this Aminoacid Sequence will "\
    "be displayed.\n\n"\
    "Invalid amino acids, such as 'U', will be filtered "\
    "out, if given.\n\n"\
    "Note that this will not necessarily "\
    "generate the same sequence, due to several different codons "\
    "encoding for the same aminoacid."
  backtrack_button.on_hover_lightblue
  @dataset[:backtrack_button] = backtrack_button
  a_quit_button = quit_button
  a_quit_button.set_name('button1')
  a_quit_button.make_bold
  @dataset[:quit_button] = a_quit_button
end

#create_left_buffer ⇒ Object

#

create_left_buffer

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 171

def create_left_buffer
  # ======================================================================= #
  # === :left_buffer
  # ======================================================================= #
  @dataset[:left_buffer] = create_text_view # The left text view.
  @dataset[:left_buffer].bblack1
  @dataset[:left_buffer].do_wrap_properly
end

#create_middle_bar_containing_the_arrow_pointing_to_the_right_side ⇒ Object

#

create_middle_bar_containing_the_arrow_pointing_to_the_right_side

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 122

def create_middle_bar_containing_the_arrow_pointing_to_the_right_side
  @middle_bar = create_vbox
  event_box = create_eventbox(
    create_label(:arrow_right)
  )
  event_box.hint =
    'This arrow can be clicked, to convert from the aminoacid sequence '\
    'to (one likely) possible DNA sequence.'
  event_box.on_clicked {
    do_determine_the_backtrack_sequence
  }
  @middle_bar.minimal(
    event_box
  )
end

#create_right_buffer ⇒ Object

#

create_right_buffer

#


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

def create_right_buffer
  # ======================================================================= #
  # === :right_buffer
  # ======================================================================= #
  @dataset[:right_buffer] = create_text_view # The right text view.
  @dataset[:right_buffer].bblack1
  @dataset[:right_buffer].do_wrap_properly
end

#create_the_boxes ⇒ Object

#

create_the_boxes

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 628

def create_the_boxes
  # ======================================================================= #
  # === @hbox1
  # ======================================================================= #
  @hbox1 = create_hbox(
    bold_text('n bacteria (start)'),
    @entry_point_start_with_n_bacteria
  )

  # ======================================================================= #
  # === @hbox2
  # ======================================================================= #
  @hbox2 = create_hbox(
    bold_text('n doubling times'),
    @entry_point_use_n_divisions
  )

  # ======================================================================= #
  # === @hbox3
  # ======================================================================= #
  @hbox3 = create_hbox(
    bold_text('n bacteria (end)'),
    @entry_point_n_cells
  )
end

#create_the_button_to_calculate_how_many_bacteria_will_exist ⇒ Object

#

create_the_button_to_calculate_how_many_bacteria_will_exist (button tag)

#


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

def create_the_button_to_calculate_how_many_bacteria_will_exist
  # ======================================================================= #
  # === @button_to_calculate_how_many_bacteria_will_exist
  # ======================================================================= #
  @button_to_calculate_how_many_bacteria_will_exist = bold_button(
    '_Calculate how many bacteria will exist after n rounds',
    self,
    :use_mnemonic
  ) {
    :do_the_calculation
  }
  @button_to_calculate_how_many_bacteria_will_exist.clear_background
  @button_to_calculate_how_many_bacteria_will_exist.bblack2
  @button_to_calculate_how_many_bacteria_will_exist.hint =
    "Click on this button in order to do the calculation\n"\
    "e. g. <b>how many bacteria we will have</b> "\
    "based on the above parameters."
  @button_to_calculate_how_many_bacteria_will_exist.on_hover(:powderblue)
end

#create_the_buttons ⇒ Object

#

create_the_buttons (buttons tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 421

def create_the_buttons
  create_the_button_to_calculate_how_many_bacteria_will_exist
end

#create_the_entries ⇒ Object

#

create_the_entries (entry tag, entries tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 567

def create_the_entries
  # ======================================================================= #
  # === @entry_point_start_with_n_bacteria
  # ======================================================================= #
  @entry_point_start_with_n_bacteria = create_entry
  @entry_point_start_with_n_bacteria.default = 10
  @entry_point_start_with_n_bacteria.bblack1
  @entry_point_start_with_n_bacteria.on_click_select_all
  @entry_point_start_with_n_bacteria.do_center
  @entry_point_start_with_n_bacteria.on_key_press_event { |widget, event|
    if use_gtk3?
      do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
    else
      do_the_calculation
    end
  }
  @entry_point_start_with_n_bacteria.hint =
    'Input a <b>number</b> here, denoting how many bacteria '\
    'exist at the start.'

  # ======================================================================= #
  # === @entry_point_use_n_divisions
  # ======================================================================= #
  @entry_point_use_n_divisions = create_entry
  @entry_point_use_n_divisions.default = 10
  @entry_point_use_n_divisions.bblack1
  @entry_point_use_n_divisions.on_click_select_all
  @entry_point_use_n_divisions.do_center
  @entry_point_use_n_divisions.on_key_press_event { |widget, event|
    if use_gtk3?
      do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
    else
      do_the_calculation
    end
  }
  @entry_point_use_n_divisions.hint =
    'Input a <b>number</b> here, denoting how many cell '\
    'divisions the bacteria will undergo.'

  # ======================================================================= #
  # === @entry_point_n_cells
  # ======================================================================= #
  @entry_point_n_cells = create_entry
  @entry_point_n_cells.default = 0
  @entry_point_n_cells.bblack1
  @entry_point_n_cells.do_center
  @entry_point_n_cells.on_key_press_event { |widget, event|
    if use_gtk3?
      do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
    else
      do_the_calculation
    end
  }
  @entry_point_n_cells.hint =
    'The number here will be <b>the amount of bacteria '\
    'after n cell divisions</b>.'
end

#create_the_hspacer ⇒ Object

#

create_the_hspacer

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 657

def create_the_hspacer
  @a_hspacer = create_hspacer
end

#create_the_scrolled_window ⇒ Object

#

create_the_scrolled_window

#


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

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_single_treeview ⇒ Object

#

create_the_single_treeview

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 458

def create_the_single_treeview
  @treeview = create_tree_view(@list_store) { :clickable_headers }
  @treeview.set_name('custom_treeview')
  @treeview.headers('Aminoacid','n times')
  @treeview.clickable_headers
  @treeview.set_enable_search(true)
  @treeview.set_reorderable(true)
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 334

def create_the_skeleton
  @main_vbox = vbox
  create_buttons
  create_left_buffer  # Our left buffer.
  create_right_buffer # Our right buffer.
  create_top_hbox     # This should come after the two buffers.
  create_middle_bar_containing_the_arrow_pointing_to_the_right_side
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/aminoacid_composition/aminoacid_composition.rb', line 234

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

#create_the_treeviews ⇒ Object

#

create_the_treeviews

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 399

def create_the_treeviews
  # ======================================================================= #
  # === @list_store
  # ======================================================================= #
  @list_store = create_liststore(String, String)
  # ======================================================================= #
  # Sort the number of aminoacids a bit differently.
  # ======================================================================= #
  @list_store.set_sort_func(1) { |_model, iter1, iter2|
    iter2[1].to_i <=> iter1[1].to_i
  }
  create_the_single_treeview
  columns = @treeview.columns?
  columns[0].allow_resizing
  columns[1].allow_resizing
  columns[0].sortable_based_on(0)
  columns[1].sortable_based_on(1)
end

#create_then_add_the_header_bar ⇒ Object

#

create_then_add_the_header_bar

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 344

def create_then_add_the_header_bar
  require 'bioroebe/gui/universal_widgets/aminoacid_composition/customized_dialog.rb'
  header = return_default_header_bar
  label_description = text(TITLE)
  label_description.make_bold
  header.set_custom_title(label_description)

  header.spacing = 10
  header.bblack1

  button = button_themed_icon('edit-paste-symbolic.symbolic')
  button.hint = 'Click this button to show more information '\
                'about this application.'
  content = <<-EOF
This widget will operate via the following <b>aminoacid weights</b>,
in Dalton, without the weight of a H₂O water molecule (18g/mol):

EOF
  content = content.dup
  YAML.load_file(Bioroebe.file_molecular_weight).each_pair {|key, value|
    content << "   <b>#{key}</b>: "\
               "<span color=\"steelblue\">#{value.to_s.rjust(6)}</span>\n"
  }
  content << "
 Compare with this URL:\n
   <a href=\"https://www.selleckchem.com/peptide-calculator.html\" title=\"Another useful resource\">https://www.selleckchem.com/peptide-calculator.html</a>
  "
  text_widget = left_aligned_text(content)
  text_widget.use_this_font = :hack_18
  button.on_clicked {
    ::Bioroebe::GUI::Gtk::CustomizedDialog.new(text_widget)
  }
  header.pack_start(button)
  minimal(header, 2)
end

#create_top_hbox ⇒ Object

#

create_top_hbox

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 141

def create_top_hbox
  # ======================================================================= #
  # The paned-widget is close to the top.
  # ======================================================================= #
  scrolled_window_right = scrolled_window(right_buffer?)
  scrolled_window_right.clear_background
  scrolled_window_right.width_height(300, 300)
  scrolled_window_right.bblack1
  scrolled_window_right.mar2px
  # ======================================================================= #
  # === scrolled_window_left
  # ======================================================================= #
  scrolled_window_left  = scrolled_window(left_buffer?)
  scrolled_window_left.clear_background
  scrolled_window_left.width_height(300, 300)
  scrolled_window_left.bblack1
  scrolled_window_left.mar2px
  top_hpaned = gtk_hpaned(
    scrolled_window_left,
    scrolled_window_right
  ) {{ border_width: 10 }}
  this_position = (width?.to_f / 1.5).to_i
  top_hpaned.set_position(this_position)
  top_hpaned.show_all
  @dataset[:top_hbox] = top_hpaned
end

#create_user_input ⇒ Object

#

create_user_input

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 301

def create_user_input
  # ======================================================================= #
  # === @entry_input_sequence
  # ======================================================================= #
  @entry_input_sequence = create_entry
  @entry_input_sequence.hint =
    "Input your aminoacid sequence here, then hit the enter-key to "\
    "evaluate the given input. Invalid entries (aka <b>non-aminoacids</b>) "\
    "will be filtered away, so do not be surprised if the sequence may "\
    "be modified (== <b>sanitized</b>).\n\n"\
    "The cursor-position will indicate at which aminoacid "\
    "position we are at.\n"
  @entry_input_sequence.yellow_background
  @entry_input_sequence.css_class('pad4px')
  @entry_input_sequence.signal_connect(:event) {|widget, event|
    if is_mouse_button_release_event?(event)
      update_information_deduced_from_the_aminoacid_sequence
    end
  }
end

#do_create_a_new_fasta_file ⇒ Object

#

do_create_a_new_fasta_file

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 512

def do_create_a_new_fasta_file
  what = @entry_input_sequence.text?.dup
  what.prepend(
    "> Random aminoacid sequence generated via a ruby-gtk3 "\
    "GUI (#{what.size} aminoacids)\n"
  )
  into = path_to_the_fasta_file?
  ::Bioroebe.write_what_into(what, into)
  vbox1 = gtk_vbox
  use_this_as_the_label = text(
    "Created a new file at:\n"
  )
  vbox1.minimal(use_this_as_the_label, 5)
  vbox1.width_height(600, 400)
  entry1 = gtk_bold_entry(into)
  entry1.deselect
  entry1.width_height(300, 30)
  entry1.light_yellowish_background
  vbox1.minimal(entry1, 5)
  use_this_as_the_label.deselect
  popup_over_this_widget(
    @event_box1,
    vbox1
  ).popup
end

#do_determine_the_backtrack_sequence ⇒ Object Also known as: do_determine_the_DNA_sequence

#

do_determine_the_backtrack_sequence (click tag)

This will do what is necessary to find the backtrack sequence.

#


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

def do_determine_the_backtrack_sequence
  filter_away_invalid_aminoacids_from_the_left_buffer
  _ = left_buffer?.text?.to_s
  _.upcase!
  _ = ::Bioroebe.remove_invalid_aminoacids(_)
  left_buffer?.set_text(_)
  # ======================================================================= #
  # Ok, now we can determine the right hand side:
  # ======================================================================= #
  text_for_right_hand_side = ::Bioroebe::ProteinToDNA.new(_, :be_quiet).dna_sequence?
  right_buffer?.set_text(text_for_right_hand_side)
end

#do_open_a_local_FASTA_file(this_widget = @parent_widget) ⇒ Object

#

do_open_a_local_FASTA_file

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 664

def do_open_a_local_FASTA_file(
    this_widget = @parent_widget
  )
  require 'gtk_paradise/widgets/gtk3/select_file/select_file.rb'
  # ======================================================================= #
  # We will actively filter for .mp3 files only.
  # ======================================================================= #
  widget = ::Gtk::SelectFile.new(this_widget) {{
    filter_for_these_file_types: '.fasta',
    current_folder:              ::Bioroebe.log_dir?+'fasta/'
  }}
  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.
    require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
    dataset = File.read(this_file)
    _ = Bioroebe::ParseFasta.new
    unless dataset.start_with?('--')
      _.set_data(dataset) # This will use the default file.
      _.split_into_proper_sections
      set_main_entry(_.body?)
      fill_with_this(_.body?)
      do_update_the_widget_on_the_right_side
    end
  end
  return this_file
end

#do_the_calculation ⇒ Object

#

do_the_calculation

This method will do the actual calculation part.

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 290

def do_the_calculation
  result = ::Bioroebe.calculate_exponential_growth(
    number_of_cells     = @entry_point_start_with_n_bacteria.text?,
    number_of_divisions = @entry_point_use_n_divisions.text?
  )
  @entry_point_n_cells.set_text(result.to_s)
end

#fill_the_table_data_with_this_sequence(i = @entry_input_sequence.text?) ⇒ Object Also known as: fill_with_this

#

fill_the_table_data_with_this_sequence

#


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

def fill_the_table_data_with_this_sequence(
    i = @entry_input_sequence.text?
  )
  @list_store.clear
  hash = Bioroebe.return_composition_from_this_aminoacid_sequence(i)
  array = hash.to_a.map {|inner_array| inner_array.map {|entry| entry.to_s }}
  ::Gtk.populate_this_liststore(@list_store, array) if use_gtk3?
end

#filter_away_invalid_aminoacids(i) ⇒ Object

#

filter_away_invalid_aminoacids

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 147

def filter_away_invalid_aminoacids(i)
  ::Bioroebe.filter_away_invalid_aminoacids(i)
end

#filter_away_invalid_aminoacids_from_the_left_buffer ⇒ Object

#

filter_away_invalid_aminoacids_from_the_left_buffer

This method is used to “sanitize” the input - invalid aminoacids are flat out removed.

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 277

def filter_away_invalid_aminoacids_from_the_left_buffer
  _ = left_buffer?.text?.to_s
  possible_new_text = Bioroebe.strict_filter_away_invalid_aminoacids(_)
  unless _ == possible_new_text
    left_buffer?.set_text(possible_new_text)
  end
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/protein_to_DNA/protein_to_DNA.rb', line 197

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

#custom_treeview.view header button {
background-color: white;
color: royalblue;
font-weight: bold;
font-size: larger;
padding: 8px;
}'
  apply_the_CSS_rules
end

#left_buffer? ⇒ Boolean Also known as: left?

#

left_buffer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 309

def left_buffer?
  @dataset[:left_buffer]
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 183

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/protein_to_DNA/protein_to_DNA.rb', line 215

def menu(i = nil)
  if i
    if i.is_a? Array
      i.each {|entry| menu(entry) }
    else
      case i # case tag
      when ''
      end
    end
  end
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 230

def padding?
  2
end

#path_to_the_fasta_file? ⇒ Boolean

#

path_to_the_fasta_file?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 383

def path_to_the_fasta_file?
  ::Bioroebe.log_dir?+
  'fasta/aminoacid_sequence.fasta'
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 82

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?
  set_label_widget(
    create_label.set_markup(
      %Q(<span foreground="#000000" weight="bold">#{TITLE}</span>)
    )
  ) if respond_to?(:set_label_widget) and use_gtk3? # Do this after handle_CSS().
  # ======================================================================= #
  # === @dataset
  # ======================================================================= #
  @dataset = {}
end

#return_how_many_aminoacids_are_in_the_sequence(i = @entry_user_input) ⇒ Object

#

return_how_many_aminoacids_are_in_the_sequence

#


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

def return_how_many_aminoacids_are_in_the_sequence(
    i = @entry_user_input
  )
  return 'This sequence has '+i.text?.to_s.size.to_s+' aminoacids.'
end

#return_the_first_row ⇒ Object

#

return_the_first_row

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 209

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

#return_widget_containing_the_toolbox_images ⇒ Object

#

return_widget_containing_the_toolbox_images

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 493

def return_widget_containing_the_toolbox_images
  hbox = create_hbox
  @event_box1 = create_event_box(
    image_folder_visiting_symbolic
  )
  @event_box1.hint =
    "Click on this image to create a new local "\
    ".fasta file with that sequence.\n\nThe location will be "\
    "at: <b>#{path_to_the_fasta_file?}</b>"
  @event_box1.on_clicked {
    do_create_a_new_fasta_file
  }
  hbox.minimal(@event_box1, 4)
  return hbox
end

#right_buffer? ⇒ Boolean Also known as: right?

#

right_buffer?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 288

def right_buffer?
  @dataset[:right_buffer]
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 346

def run
  run_super
end

#set_aminoacid_sequence(i) ⇒ Object

#

set_aminoacid_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 295

def set_aminoacid_sequence(i)
  @dataset[:left_buffer].set_text(i.to_s)
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/aminoacid_composition/aminoacid_composition.rb', line 177

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/aminoacid_composition/aminoacid_composition.rb', line 184

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/aminoacid_composition/aminoacid_composition.rb', line 325

def set_parent_widget(i)
  @parent_widget = i
end

#simulate_enter_click(_ = @entry_input_sequence.text?) ⇒ Object Also known as: update_information_deduced_from_the_aminoacid_sequence, do_update_the_widget_on_the_right_side

#

simulate_enter_click

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 541

def simulate_enter_click(
    _ = @entry_input_sequence.text?
  )
  _.upcase!
  # ======================================================================= #
  # First weed out all invalid aminoacids:
  # ======================================================================= #
  _ = 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 of these aminoacids is: <b>'+
    calculated_weight?(_).to_s+'</b> Dalton'
  )
  @label_molecular_weight.do_markify
  update_label_cursor_position
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/protein_to_DNA/protein_to_DNA.rb', line 190

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/aminoacid_composition/aminoacid_composition.rb', line 282

def smaller_font?
  SMALLER_FONT
end

#textview? ⇒ Boolean

#

textview?

#

Returns:

  • (Boolean) 


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

def textview?
  @text_view
end

#top_hbox? ⇒ Boolean

#

top_hbox?

#

Returns:

  • (Boolean) 


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

def top_hbox?
  @dataset[:top_hbox]
end

#update_label_cursor_position ⇒ Object

#

update_label_cursor_position

#


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# File 'lib/bioroebe/gui/universal_widgets/aminoacid_composition/aminoacid_composition.rb', line 132

def update_label_cursor_position
  cursor_position = @entry_input_sequence.cursor_position
  character = @entry_input_sequence.text?[cursor_position, 1].to_s
  unless character.empty?
    _ = 'The aminoacid at position <b>'+
        (cursor_position+1).to_s+
        '</b> is: <b>'+character.to_s+'</b>.'
    @label_cursor_position.set_text(_)
    @label_cursor_position.do_markify
  end
end