Class: Bioroebe::GUI::UniversalWidgets::Controller

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

Overview

Bioroebe::GUI::UniversalWidgets::Controller

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this small widget.

The old title before the rewrite in February 2022 was this String:

'Graphical Interface to the Bioroebe project'
#
'Controller'
WIDTH =
#

WIDTH

#
'65% or 600px minimum'
HEIGHT =
#

HEIGHT

#
'55% or 400px minimum'
MONOSPACED_FONT =
#

MONOSPACED_FONT

When this font is changed, don’t forget to also change the font at SMALLER_FONT.

#
:hack_20
USE_THIS_FONT = 
MONOSPACED_FONT
SMALLER_FONT =
#

SMALLER_FONT

#
:hack_16
USE_THIS_SLIGHTLY_SMALLER_FONT =
#

USE_THIS_SLIGHTLY_SMALLER_FONT

#
:hack_16
HASH_DESIGNATED_KEY_COMBINATIONS =
#

HASH_DESIGNATED_KEY_COMBINATIONS

#
{
  'alt+1': 'key_pressed(1)',
  'alt+2': 'key_pressed(2)',
  'alt+3': 'key_pressed(3)',
  'alt+4': 'key_pressed(4)',
  'alt+5': 'key_pressed(5)',
  'alt+6': 'key_pressed(6)',
  'alt+7': 'key_pressed(7)',
  'alt+8': 'key_pressed(8)',
  'alt+9': 'key_pressed(9)',
  'alt+0': 'key_pressed(0)'
}

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) ⇒ Controller

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 94

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::Controller[]

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 439

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::Controller.run

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 446

def self.run(
    i = ARGV
  )
  _ = ::Bioroebe::GUI::Gtk::Controller.new(i) 
  r = ::Gtk.runner_factory(_)
  r.background_colour :white
  r.add_accel_group(@accel_group = ::Gtk::AccelGroup.new)
  _.set_parent_widget(r)
  _.enable_these_key_combinations(
    _::HASH_DESIGNATED_KEY_COMBINATIONS
  )
  return r
end

Instance Method Details

#batch_require_all_relevant_gtk3_files ⇒ Object

#

batch_require_all_relevant_gtk3_files

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 249

def batch_require_all_relevant_gtk3_files
  require 'bioroebe/gui/gtk3/alignment/alignment.rb'
  require 'bioroebe/gui/gtk3/nucleotide_analyser/nucleotide_analyser.rb'
  require 'bioroebe/gui/gtk3/aminoacid_composition/aminoacid_composition.rb'
  require 'bioroebe/gui/gtk3/blosum_matrix_viewer/blosum_matrix_viewer.rb'
  require 'bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
  require 'bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.rb'
  require 'bioroebe/gui/gtk3/fasta_table_widget/fasta_table_widget.rb'
  require 'bioroebe/gui/gtk3/format_converter/format_converter.rb'
  require 'bioroebe/gui/gtk3/gene/gene.rb'
  require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
  require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
  require 'bioroebe/gui/gtk3/parse_pdb_file/parse_pdb_file.rb'
  require 'bioroebe/gui/gtk3/primer_design_widget/primer_design_widget.rb'
  require 'bioroebe/gui/gtk3/protein_to_DNA/protein_to_DNA.rb'
  require 'bioroebe/gui/gtk3/random_sequence/random_sequence.rb'
  require 'bioroebe/gui/gtk3/restriction_enzymes/restriction_enzymes.rb'
  require 'bioroebe/gui/gtk3/show_codon_table/show_codon_table.rb'
  require 'bioroebe/gui/gtk3/show_codon_usage/show_codon_usage.rb'
  require 'bioroebe/gui/gtk3/sizeseq/sizeseq.rb'
  require 'bioroebe/gui/gtk3/three_to_one/three_to_one.rb'
end

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 139

def border_size?
  1
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 313

def connect_the_skeleton
  abort_on_exception

  # ========================================================================= #
  # === DnaToAminoacidWidget
  # ========================================================================= #
  @dna_to_aminoacid_widget = DnaToAminoacidWidget.new
  @dna_to_aminoacid_widget.set_parent_widget(self)
  @notebook.add_page('dna-to-aminoacid-widget', vbox(@dna_to_aminoacid_widget))
  # ======================================================================= #
  # === nucleotide-analyser
  # ======================================================================= #
  @notebook.add_page('nucleotide-analyser', vbox(@nucleotide_analyser))
  # ======================================================================= #
  # === aminoacid-composition
  # ======================================================================= #
  @aminoacid_composition = AminoacidComposition.new
  @aminoacid_composition.set_parent_widget(self)
  @notebook.add_page('aminoacid-composition', vbox(@aminoacid_composition))
  # ======================================================================= #
  # === protein-to-DNA
  # ======================================================================= #
  @protein_to_DNA = ProteinToDNA.new
  @notebook.add_page('protein-to-DNA', vbox(@protein_to_DNA))
  # ======================================================================= #
  # === dna-to-reverse-complement
  # ======================================================================= #
  @notebook.add_page('dna-to-reverse-complement', vbox(DnaToReverseComplementWidget.new))
  # ======================================================================= #
  # === alignment
  # ======================================================================= #
  @notebook.add_page('alignment', vbox(Alignment.new))
  # ======================================================================= #
  # === anti-sense-strand
  #
  # Not added - it is not sufficiently useful.
  # ======================================================================= #
  # ======================================================================= #
  # === blosum-matrix-viewer
  # ======================================================================= #
  @notebook.add_page('blosum-matrix-viewer', vbox(BlosumMatrixViewer.new))
  # ======================================================================= #
  # === calculate_cell_numbers_of_bacteria
  #
  # This one is skipped too - end users do not really need it.
  # ======================================================================= #
  # ======================================================================= #
  # === fasta-table-widget
  # ======================================================================= #
  @notebook.add_page('fasta-table-widget', vbox(FastaTableWidget.new))
  # ======================================================================= #
  # === format-converter
  # ======================================================================= #
  @notebook.add_page('format-converter', vbox(FormatConverter.new))
  # ======================================================================= #
  # === gene
  # ======================================================================= #
  @notebook.add_page('gene', vbox(Gene.new))
  # ======================================================================= #
  # === hamming-distance
  # ======================================================================= #
  @notebook.add_page('hamming-distance', vbox(HammingDistance.new))
  # ======================================================================= #
  # === levensthein-distance
  # ======================================================================= #
  @notebook.add_page('levensthein-distance', vbox(LevenstheinDistance.new))
  # ======================================================================= #
  # === parse-pdb-file
  # ======================================================================= #
  @notebook.add_page('parse-pdb-file', vbox(ParsePdbFile.new))
  # ======================================================================= #
  # === primer-design-widget
  # ======================================================================= #
  @notebook.add_page('primer-design-widget', vbox(PrimerDesignWidget.new))
  # ======================================================================= #
  # === random-sequence
  # ======================================================================= #
  @notebook.add_page('random-sequence', vbox(RandomSequence.new))
  # ======================================================================= #
  # === restriction-enzymes
  # ======================================================================= #
  @notebook.add_page('restriction-enzymes', vbox(RestrictionEnzymes.new))
  # ======================================================================= #
  # === show-codon-table
  # ======================================================================= #
  @notebook.add_page('show-codon-table', vbox(ShowCodonTable.new))
  # ======================================================================= #
  # === show-codon-usage
  # ======================================================================= #
  @notebook.add_page('show-codon-usage', vbox(ShowCodonUsage.new))
  # ======================================================================= #
  # === sizeseq
  # ======================================================================= #
  @notebook.add_page('sizeseq', vbox(Sizeseq.new))
  # ======================================================================= #
  # === three-to-one
  # ======================================================================= #
  @notebook.add_page('three-to-one', vbox(ThreeToOne.new))
  # ======================================================================= #
  # === www-finder
  #
  # This one is currently not in use. Perhaps at some later moment
  # in time we will add hyperlinks that may be useful, but right
  # now we will not.
  # ======================================================================= #
  draggable_one = draggable_via_up_and_down_movement(header_bar?, @notebook)

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

  ::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_the_header_bar ⇒ Object

#

create_the_header_bar (header tag, top tag)

#


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

def create_the_header_bar
  # ======================================================================= #
  # === @header_bar
  # ======================================================================= #
  @header_bar = default_header_bar
  @header_bar.pad8px
  _ = selectable_text(' 🐟  Controller  🐟 ')
  @header_bar.central_element(_)
end

#create_the_notebook ⇒ Object

#

create_the_notebook (notebook tag)

#


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

def create_the_notebook
  # ======================================================================= #
  # === @notebook
  # ======================================================================= #
  @notebook = create_notebook
  @notebook.enable_popup = true
  @notebook.use_this_font(smaller_font?)
  @notebook.set_border_width(5)
  @notebook.do_show_border
  @notebook.pad8px
  @notebook.bblack1
  @notebook.is_scrollable
  @notebook.position_on_top
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 175

def create_the_skeleton
  create_the_header_bar
  create_the_notebook
end

#do_batch_load_all_gtk3_related_ruby_files ⇒ Object

#

This method is currently not in use. It was used up until February 2022 to batch-load all ruby-gtk3 related files.

#


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

def do_batch_load_all_gtk3_related_ruby_files
  base_dir_to_use = Bioroebe.project_directory?+'gui/gtk3/'
  all_entries = Dir[base_dir_to_use+'*']
  all_entries.select {|entry| File.directory? entry }.each {|entry|
    next if entry.end_with? 'notebook' # Exclude self.
    entry = File.basename(entry).delete_suffix('.rb')
    load_this_file = "#{base_dir_to_use}#{entry}/#{entry}.rb"
    require load_this_file
  }
end

#focus_on_tab(number = 1) ⇒ Object Also known as: key_pressed

#

focus_on_tab

#


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

def focus_on_tab(
    number = 1
  )
  @notebook.focus_on_tab(number.to_i - 1)
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/controller/controller.rb', line 160

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '
notebook header {
    color: green;
    border: 2px dotted royalblue;
  }
  '
  apply_the_CSS_rules
end

#header_bar? ⇒ Boolean

#

header_bar?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 225

def header_bar?
  @header_bar
end

#main_dna_sequence? ⇒ Boolean Also known as: main_DNA_sequence?

#

main_dna_sequence?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 202

def main_dna_sequence?
  @dna_to_aminoacid_widget.dna_sequence?
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 146

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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

def padding?
  2
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 109

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?
  # ======================================================================= #
  # === @nucleotide_analyser
  # ======================================================================= #
  @nucleotide_analyser = NucleotideAnalyser.new
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 306

def run
  run_super
end

#set_aminoacid_sequence(i) ⇒ Object

#

set_aminoacid_sequence

#


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

def set_aminoacid_sequence(i)
  i = i.to_s
  @aminoacid_sequence = i
  @aminoacid_composition.set_main_input_sequence_and_evaluate_it(i)
  @protein_to_DNA.set_aminoacid_sequence(i)
  if @protein_to_DNA.respond_to? :do_determine_the_DNA_sequence
    @protein_to_DNA.do_determine_the_DNA_sequence
  end
  # ======================================================================= #
  # Also update the nucleotide-analyser next:
  # ======================================================================= #
  @nucleotide_analyser.set_dna_sequence(
    main_dna_sequence?.delete(' ')
  )
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/controller/controller.rb', line 153

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/controller/controller.rb', line 218

def smaller_font?
  SMALLER_FONT
end