Class: Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser

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

Overview

Bioroebe::GUI::UniversalWidgets::NucleotideAnalyser

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this widget.

#
'Nucleotide Analyser'
WIDTH =
#

WIDTH

#
'75% or 1200px 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_22
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
USE_THIS_HEADER =
#

USE_THIS_HEADER

#
['one-letter abbreviation', 'n times']
GENERATE_N_AMINOACIDS_BY_DEFAULT =
#

GENERATE_N_AMINOACIDS_BY_DEFAULT

#
15
COLOUR_FOR_NON_MATCHES =
#

COLOUR_FOR_NON_MATCHES

This is the colour that will be used for non-matching nucleotides.

#
:magenta

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) ⇒ NucleotideAnalyser

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 96

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::NucleotideAnalyser[]

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 545

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::NucleotideAnalyser.run

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 552

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::NucleotideAnalyser.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/nucleotide_analyser/nucleotide_analyser.rb', line 391

def border_size?
  2
end

#clear_table ⇒ Object

#

clear_table

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 224

def clear_table
  @list_store.clear
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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

def connect_the_skeleton
  abort_on_exception
  
  @outer_vbox = create_vbox
  
  _ = first_argument?.to_s
  @outer_vbox.minimal(@entry_input_sequence, 2)
  @entry_input_sequence.set_text(@sequence.to_s)
  @outer_vbox.minimal(@text_this_sequence_contains, 2)
  @outer_vbox.minimal(horizontal_spacer)
  @tree_view.all_are_sortable # Make them all sortable.
  scrolled_window = create_scrolled_window(@tree_view) { :never_always }
  scrolled_window.set_size_request(420, 260)
  @outer_vbox.minimal(scrolled_window, 5)
  @outer_vbox.minimal(gtk_horizontal_spacer)
  update_the_labels
  @outer_vbox.minimal(@label_GC_content)
  @outer_vbox.minimal(@label_AT_content)
  hbox = create_hbox
  hbox.maximal(@button_reset,                    1)
  hbox.maximal(@button_reset_the_input_sequence, 1)
  hbox.maximal(@button_open_file,                1)
  @outer_vbox.minimal(hbox, 2)

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

#create_the_buttons ⇒ Object

#

create_the_buttons (buttons tag, button tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 348

def create_the_buttons
  # ======================================================================= #
  # === @button_reset
  # ======================================================================= #
  @button_reset = button('_Reset the table')
  @button_reset.hint = 'This button will clear the table-result '\
                       'shown above.'
  @button_reset.on_clicked {
    clear_table
  }
  # ======================================================================= #
  # === @button_reset_the_input_sequence
  # ======================================================================= #
  @button_reset_the_input_sequence = button('Reset the _input sequence')
  @button_reset_the_input_sequence.enable_markup
  @button_reset_the_input_sequence.hint = 'This button will '\
    'reset (aka clear) the input sequence. The input sequence is kept '\
    'on top of this widget, as a gtk-entry.'
  @button_reset_the_input_sequence.on_clicked {
    do_reset_the_input_sequence
  }
  # ======================================================================= #
  # === @button_open_file
  # ======================================================================= #
  @button_open_file = button('_Open file')
  @button_open_file.enable_markup
  @button_open_file.hint = 'This button can be used to open a local'\
                           'file, typically a FASTA (.fasta) file.'
  @button_open_file.on_clicked {
    do_open_a_local_file
  }
end

#create_the_entries ⇒ Object

#

create_the_entries (entry tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 137

def create_the_entries
  # ======================================================================= #
  # === @entry_input_sequence
  # ======================================================================= #
  @entry_input_sequence = entry
  @entry_input_sequence.default_values
  @entry_input_sequence.hint = 'The sequence will be evaluated '\
    'whenever it is changed, as-is. Hit the <b>enter</b> key '\
    'to change it, for convenience.'
  @entry_input_sequence.on_changed {
    update_the_main_sequence_variable
    update_this_sequence_contains_n_nucleotides
    update_the_table_dataset
    update_the_labels
  }
  # ======================================================================= #
  # Act on when the user hits the enter-key.
  # ======================================================================= #
  @entry_input_sequence.on_enter_key {
    sanitize_the_sequence
    do_analyse_the_sequence
    update_this_sequence_contains_n_nucleotides(
      return_how_many_nucleotides_this_sequence_contains
    )
  }
end

#create_the_labels ⇒ Object

#

create_the_labels

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 430

def create_the_labels
  # ======================================================================= #
  # === @label_GC_content
  # ======================================================================= #
  @label_GC_content = left_aligned_label
  @label_GC_content.make_selectable
  # ======================================================================= #
  # === @label_AT_content
  # ======================================================================= #
  _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
  @label_AT_content = left_aligned_label(
    'The <b>AT content</b> (A+T) is: <b>'+
    (100.0 - _.to_f).round(1).to_s+'%</b>'
  )
  @label_AT_content.make_selectable
  # ======================================================================= #
  # === @text_this_sequence_contains
  # ======================================================================= #
  @text_this_sequence_contains = left_aligned_label
  @text_this_sequence_contains.make_selectable
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 455

def create_the_skeleton
  create_the_labels
  create_the_entries
  create_the_buttons
end

#dna_sequence? ⇒ Boolean

#

dna_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 174

def dna_sequence?
  @entry_input_sequence.text?
end

#do_analyse_the_sequence ⇒ Object Also known as: update_the_table_dataset

#

do_analyse_the_sequence

#


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

def do_analyse_the_sequence
  clear_table
  _ = return_dataset_based_on_this_sequence.each_slice(3).to_a
  # ======================================================================= #
  # The first element contains the header, which is not necessary.
  # ======================================================================= #
  _.shift 
  populate_this_list_store3(
    @list_store, _.compact
  )
end

#do_open_a_local_file ⇒ Object

#

do_open_a_local_file

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 246

def do_open_a_local_file
  _ = open_local_file # Find a local file. (open tag)
  if File.exist?(_) and File.file?(_)
    # ===================================================================== #
    # Handle FASTA files a bit differently next:
    # ===================================================================== #
    if _.end_with?('.fasta') or _.end_with?('.fa')
      content_of_the_file = Bioroebe.parse_fasta(_).body?
    else
      content_of_the_file = File.read(_).to_s
    end
    set_main_entry(content_of_the_file)
  end
end

#do_reset_the_input_sequence ⇒ Object

#

do_reset_the_input_sequence

#


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

def do_reset_the_input_sequence
  @entry_input_sequence.clear
end

#do_style_all_buttons_in_a_uniform_manner ⇒ Object

#

do_style_all_buttons_in_a_uniform_manner

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 200

def do_style_all_buttons_in_a_uniform_manner
  return_all_buttons.each {|this_button|
    this_button.bblack1
  }
end

#entry_input_sequence? ⇒ Boolean Also known as: main_entry?

#

entry_input_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 167

def entry_input_sequence?
  @entry_input_sequence
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/nucleotide_analyser/nucleotide_analyser.rb', line 412

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

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

#initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets(i = @sequence) ⇒ Object

#

initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets

#


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

def initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets(
    i = @sequence
  )
  # ======================================================================= #
  # Specify the dataset that we wish to use for the gtk_table3() call.
  # ======================================================================= #
  @dataset = return_dataset_based_on_this_sequence(i)
  @tree_view, @list_store = gtk_table3(
    @dataset
  ) {{
    cell_renderer_text1: :align_to_the_middle,
    cell_renderer_text2: :align_to_the_middle
  }}
  @tree_view.bblack2
  @tree_view.pad10px
  @tree_view.set_name('custom_treeview')
  @tree_view.first_column?.center
  @tree_view.second_column?.center
  @tree_view.the_headers_can_be_moved
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 398

def main_font?
  USE_THIS_FONT
end

#open_local_file ⇒ Object

#

open_local_file

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 231

def open_local_file
  # ======================================================================= #
  # We will actively filter for .mp3 files only.
  # ======================================================================= #
  widget = ::Gtk::SelectFile.new(self) {{
    current_folder: ::Bioroebe.log_dir?
  }}
  this_file = widget.do_pick_file.text.to_s
  return this_file
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 384

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 111

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?
  # ======================================================================= #
  # === @sequence
  # ======================================================================= #
  @sequence = 'GCTATGCATGCATGCTTTTTTTTTTTAGTCAGTCAGTCGATGCATGC'\
              'ATGCTAGTCAGTCAGTCGATGTGCATGCTAGTCAGTCAGTCGATGCA'
  # ^^^ overrule for now.
  initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
end

#return_dataset_based_on_this_sequence(sequence = @entry_input_sequence.text?) ⇒ Object

#

return_dataset_based_on_this_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 275

def return_dataset_based_on_this_sequence(
    sequence = @entry_input_sequence.text?
  )
  total = sequence.size
  dataset = [ # First three entries are the header.
    'Nucleotide','amount','Percentage',
    'A', sequence.count('A').to_s, ((sequence.count('A').to_f * 100) / total).round(1).to_s+'%',
    'T', sequence.count('T').to_s, ((sequence.count('T').to_f * 100) / total).round(1).to_s+'%',
    'C', sequence.count('C').to_s, ((sequence.count('C').to_f * 100) / total).round(1).to_s+'%',
    'G', sequence.count('G').to_s, ((sequence.count('G').to_f * 100) / total).round(1).to_s+'%'
  ]
  return dataset
end

#return_how_many_nucleotides_this_sequence_contains(i = @entry_input_sequence.text?) ⇒ Object

#

return_how_many_nucleotides_this_sequence_contains

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 292

def return_how_many_nucleotides_this_sequence_contains(
    i = @entry_input_sequence.text?
  )
  "This sequence contains <b>#{i.size.to_s}</b> nucleotides."
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 464

def run
  run_super
end

#sanitize_the_sequence ⇒ Object

#

sanitize_the_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 308

def sanitize_the_sequence
  if @entry_input_sequence.text?
    if @entry_input_sequence.text?.include? '-'
      new_sequence = @entry_input_sequence.text?.delete('-')
      @sequence = new_sequence
      @entry_input_sequence.set_text(new_sequence)
      @dataset = return_dataset_based_on_this_sequence(@entry_input_sequence.text?)
    end
  end
end

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

#

set_main_entry

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 341

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

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 405

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/nucleotide_analyser/nucleotide_analyser.rb', line 471

def smaller_font?
  SMALLER_FONT
end

#update_the_AT_content_label ⇒ Object

#

update_the_AT_content_label

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 329

def update_the_AT_content_label
  _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
  @label_AT_content.set_text(
    "The <b>AT content</b> (A+T) is: <b>"\
    "#{(100.0 - _.to_f).round(1).to_s}%</b>"
  )
  @label_AT_content.do_markify
end

#update_the_GC_content_label ⇒ Object

#

update_the_GC_content_label

#


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

def update_the_GC_content_label
  _ = ::Bioroebe.gc_content(@sequence, 1) # => 50.0
  @label_GC_content.set_text(
    'The <b>GC content</b> (G+C) is: <b>'+_.to_s+'%</b>'
  )
  @label_GC_content.do_markify
end

#update_the_labels ⇒ Object

#

update_the_labels

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 192

def update_the_labels
  update_the_GC_content_label
  update_the_AT_content_label
end

#update_the_main_sequence_variable ⇒ Object

#

update_the_main_sequence_variable

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 322

def update_the_main_sequence_variable
  @sequence = @entry_input_sequence.text?.delete('-')
end

#update_this_sequence_contains_n_nucleotides(i = return_how_many_nucleotides_this_sequence_contains) ⇒ Object

#

update_this_sequence_contains_n_nucleotides

#


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# File 'lib/bioroebe/gui/universal_widgets/nucleotide_analyser/nucleotide_analyser.rb', line 264

def update_this_sequence_contains_n_nucleotides(
    i = 
      return_how_many_nucleotides_this_sequence_contains
  )
  @text_this_sequence_contains.set_text(i.to_s)
  @text_this_sequence_contains.do_markify
end