Class: Bioroebe::GUI::Gtk::AminoacidComposition

Inherits:
Gtk::Box
  • Object
show all
Includes:
Gtk::BaseModule
Defined in:
lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb

Overview

Bioroebe::GUI::Gtk::AminoacidComposition

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
'Aminoacid Composition'
WIDTH =
#

WIDTH

#
'60%'
HEIGHT =
#

HEIGHT

#
'40%'
USE_THIS_FONT =
#

USE_THIS_FONT

#
:dejavu_condensed_18
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:dejavu_condensed_16
FILE_MOLECULAR_WEIGHT =
#

FILE_MOLECULAR_WEIGHT

#
Bioroebe.file_molecular_weight

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

#initialize(commandline_arguments = ARGV, run_already = true) ⇒ AminoacidComposition

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 64

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::AminoacidComposition.run

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 304

def self.run(
    i = ARGV
  )
  require 'gtk_paradise/run'
  _ = ::Bioroebe::GUI::Gtk::AminoacidComposition.new(i)
  r = ::Gtk.run
  r << _
  r.automatic
  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/aminoacid_composition/aminoacid_composition.rb', line 100

def border_size?
  2
end

#calculated_weight?(i) ⇒ Boolean

#

calculated_weight?

This method will calculate the weight.

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 269

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_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 432

def connect_skeleton
  abort_on_exception
  create_then_add_the_header_bar
  if first? and !first?.start_with?('--')
    @entry_input_sequence.set_text(first?.to_s)
  end
  # ======================================================================= #
  # === @list_store
  # ======================================================================= #
  @list_store = gtk_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_treeview
  columns = @treeview.columns?
  columns[0].allow_resizing
  columns[1].allow_resizing
  columns[0].sortable_based_on(0)
  columns[1].sortable_based_on(1)
  hbox = gtk_hbox
  hbox.maximal(@entry_input_sequence, 6)
  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_FASTA_file
  }
  hbox.minimal(event_box,       1)
  add(hbox)
  @entry_input_sequence.on_enter {
    simulate_enter_click
  }
  scrolled_window = gtk_scrolled_window(@treeview) { :always }
  scrolled_window.width_height(300, 600)
  scrolled_window.bblack1
  scrolled_window.css_class('pad2px')
  @label_n_aminoacids = left_aligned_text
  small_vbox = gtk_vbox
  small_vbox.pad4px
  small_vbox.border_width = 5
  small_vbox.minimal(@label_n_aminoacids, 4)
  @label_molecular_weight = left_aligned_text
  small_vbox.minimal(@label_molecular_weight, 3)
  @label_cursor_position = left_aligned_text
  small_vbox.minimal(@label_cursor_position,  3)
  small_vbox.minimal(return_widget_containing_the_toolbox_images, 5)
  _ = draggable_from_left_to_right(scrolled_window, small_vbox)
  _.position = 350
  minimal(_, 1)
end

#create_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 107

def create_skeleton
  create_user_input
end

#create_the_treeview ⇒ Object

#

create_the_treeview

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 489

def create_the_treeview
  @treeview = gtk_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_then_add_the_header_bar ⇒ Object

#

create_then_add_the_header_bar

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 226

def create_then_add_the_header_bar
  require 'bioroebe/gui/gtk3/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 = gtk_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_user_input ⇒ Object

#

create_user_input

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 114

def create_user_input
  # ======================================================================= #
  # === @entry_input_sequence
  # ======================================================================= #
  @entry_input_sequence = gtk_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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 377

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_open_a_local_FASTA_file(this_widget = @parent_widget) ⇒ Object

#

do_open_a_local_FASTA_file

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 346

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

#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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 145

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)
end

#handle_CSS_rules ⇒ Object

#

handle_CSS_rules (CSS tag, css tag)

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 208

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
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 180

def main_font?
  USE_THIS_FONT
end

#menu(i = commandline_arguments? ) ⇒ Object

#

menu (menu tag)

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 157

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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 93

def padding?
  6
end

#path_to_the_fasta_file? ⇒ Boolean

#

path_to_the_fasta_file?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 318

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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 79

def reset
  reset_the_internal_variables
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, NAMESPACE]
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
  handle_CSS_rules
  infer_the_size_automatically
end

#return_widget_containing_the_toolbox_images ⇒ Object

#

return_widget_containing_the_toolbox_images

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 326

def return_widget_containing_the_toolbox_images
  hbox = gtk_hbox
  @event_box1 = gtk_event_box(
    image_folder_visiting_symbolic
  )
  @event_box1.hint = 'Click on this image to create a new local '\
    '.fasta file with that sequence. The 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

#run ⇒ Object

#

run (run tag)

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 501

def run
  super()
  menu
end

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

#

set_main_entry

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 194

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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 201

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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 138

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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 406

def simulate_enter_click(
    _ = @entry_input_sequence.text?
  )
  _.upcase!
  # ======================================================================= #
  # First weed out all invalid aminoacids:
  # ======================================================================= #
  _ = ::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 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/gtk3/aminoacid_composition/aminoacid_composition.rb', line 187

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end

#update_label_cursor_position ⇒ Object

#

update_label_cursor_position

#

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# File 'lib/bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb', line 289

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