Class: Bioroebe::GUI::UniversalWidgets::Gene

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

Overview

Bioroebe::GUI::UniversalWidgets::Gene

Constant Summary collapse

TITLE =
#

TITLE

Specify which title to use for this small widget.

#
'A gene'
WIDTH =
#

WIDTH

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

HEIGHT

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

TEXT_COMPARE_THE_TWO_SEQUENCES

#
'_Compare the two sequences'
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
USE_THIS_TITLE_FOR_THE_MAIN_BUTTON =
#

USE_THIS_TITLE_FOR_THE_MAIN_BUTTON

#
'_Determine the DNA sequence'
PADDING_TO_USE =
#

PADDING_TO_USE

#
12
DEFAULT_TEXT_FOR_ENTRY1 =
#

DEFAULT_TEXT_FOR_ENTRY1

#
'AGUUCGAUGGAAAATAT'
DEFAULT_TEXT_FOR_ENTRY2 =
#

DEFAULT_TEXT_FOR_ENTRY2

#
'AGUCCGGUCGAAAAAAA'

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) ⇒ Gene

#

initialize

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 101

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::Gene[]

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 256

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

.run(i = ARGV) ⇒ Object

#

Bioroebe::GUI::Gtk::Gene.run

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 263

def self.run(
    i = ARGV
  )
  r = ::Gtk.runner_factory(
    ::Bioroebe::GUI::Gtk::Gene.new(i)
  )
  r.modify_background(:normal, :mintcream)
  return r
end

Instance Method Details

#border_size? ⇒ Boolean

#

border_size?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 143

def border_size?
  8
end

#colourize_contig(start_position = 3, end_position = 12, use_this_colour = :steelblue) ⇒ Object

#

colourize_contig

This method can be used to colourize a specific contig in the nucleotide sequence at hand.

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 236

def colourize_contig(
    start_position  =  3,
    end_position    = 12,
    use_this_colour = :steelblue
  )
  old_text = @sequence.label.to_s
  new_text = old_text.dup
  new_text[start_position, end_position] =
    '<span foreground="'+use_this_colour.to_s+'">'+
    new_text[start_position, end_position]+
    '</span>'
  @sequence.set_text(
    new_text
  )
  @sequence.parse_markup
end

#connect_the_skeleton ⇒ Object

#

connect_the_skeleton (connect tag, skeleton tag)

#


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

def connect_the_skeleton
  abort_on_exception
  
  hbox = create_hbox
  hbox.minimal(
    text("5' - ")
  )
  @sequence = text('ATGGTACGTACGTCAGTGAGTCA')
  hbox.minimal(
    @sequence
  )
  hbox.minimal(
    text(" - '3")
  )

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

  ::UniversalWidgets.set_main_window(window)
  upon_delete_event_quit_the_application

  colourize_contig

  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.set_size_request(80, 100)
  window.top_left
  run_main
end

#create_the_skeleton ⇒ Object

#

create_the_skeleton (create tag, skeleton tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 176

def create_the_skeleton
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/gene/gene.rb', line 164

def handle_CSS_rules
  use_gtk_paradise_project_css_file
  append_project_css_file
  add_these_custom_CSS_rules '

'
  apply_the_CSS_rules
end

#main_font? ⇒ Boolean

#

main_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 150

def main_font?
  USE_THIS_FONT
end

#padding? ⇒ Boolean

#

padding?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 136

def padding?
  PADDING_TO_USE
end

#reset ⇒ Object

#

reset (reset tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 116

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_border_width(5)
end

#run ⇒ Object

#

run (run tag)

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 182

def run
  run_super
end

#set_sequence(i) ⇒ Object

#

set_sequence

#


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 226

def set_sequence(i)
  @sequence.set_text("#{i}")
end

#slightly_smaller_font? ⇒ Boolean

#

slightly_smaller_font?

#

Returns:

  • (Boolean) 


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# File 'lib/bioroebe/gui/universal_widgets/gene/gene.rb', line 157

def slightly_smaller_font?
  USE_THIS_SLIGHTLY_SMALLER_FONT
end