Class: Bioroebe::GUI::Gtk::NucleotideAnalyser

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

Overview

Bioroebe::GUI::Gtk::NucleotideAnalyser

Constant Summary collapse

NAMESPACE =
#

NAMESPACE

#
inspect
TITLE =
#

TITLE

#
'Nucleotide Analyser'
WIDTH =
#

WIDTH

#
'65% or minimum 350px'
HEIGHT =
#

HEIGHT

#
580
USE_THIS_FONT =
#

USE_THIS_FONT

#
:hack_16

Class Method Summary collapse

Instance Method Summary collapse

Constructor Details

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

#

initialize

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 54

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::NucleotideAnalyser.run

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 461

def self.run(
    i = ARGV
  )
  require 'gtk_paradise/run'
  _ = ::Bioroebe::GUI::Gtk::NucleotideAnalyser.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/nucleotide_analyser/nucleotide_analyser.rb', line 122

def border_size?
  2
end

#clear_table ⇒ Object

#

clear_table

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 162

def clear_table
  @list_store.clear
end

#connect_skeleton ⇒ Object

#

connect_skeleton (connect tag)

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 303

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

#create_buttons ⇒ Object

#

create_buttons (buttons tag, button tag)

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 202

def create_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_entry ⇒ Object

#

create_entry (entry tag)

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 371

def create_entry
  # ======================================================================= #
  # === @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_skeleton ⇒ Object

#

create_skeleton (create tag)

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 129

def create_skeleton
  create_buttons
  create_the_labels
  create_entry
end

#create_the_labels ⇒ Object

#

create_the_labels

#

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

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

#dna_sequence? ⇒ Boolean

#

dna_sequence?

#

Returns:

  • (Boolean) 

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 408

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 147

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 184

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 275

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

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 401

def entry_input_sequence?
  @entry_input_sequence
end

#handle_CSS_rules ⇒ Object

#

handle_CSS_rules (CSS tag)

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 328

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_CSS_file
  append_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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 91

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

#open_local_file ⇒ Object

#

open_local_file

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 169

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 115

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 69

def reset
  reset_the_internal_variables
  # ======================================================================= #
  # === @configuration
  # ======================================================================= #
  @configuration = [true, __dir__, NAMESPACE]
  title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
  infer_the_size_automatically
  set_border_width(10)
  # ======================================================================= #
  # === @sequence
  # ======================================================================= #
  @sequence = 'GCTATGCATGCATGCTTTTTTTTTTTAGTCAGTCAGTCGATGCATGC'\
              'ATGCTAGTCAGTCAGTCGATGTGCATGCTAGTCAGTCAGTCGATGCA'
  # ^^^ overrule for now.
  initialize_dataset_based_on_the_main_sequence_and_create_the_associated_widgets
  handle_CSS_rules
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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 249

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 266

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 453

def run
  create_skeleton_then_connect_skeleton
  do_style_all_buttons_in_a_uniform_manner
end

#sanitize_the_sequence ⇒ Object

#

sanitize_the_sequence

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 282

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 446

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

#update_the_AT_content_label ⇒ Object

#

update_the_AT_content_label

#

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# File 'lib/bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 434

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 415

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 426

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 296

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/gtk3/nucleotide_analyser/nucleotide_analyser.rb', line 238

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