Class: Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget
- Inherits:
-
UniversalWidgets::Base
- Object
- UniversalWidgets::Base
- Bioroebe::GUI::UniversalWidgets::DnaToAminoacidWidget
show all
- Includes:
- CommandlineArguments, Bioroebe::GUI
- Defined in:
- lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb
Overview
Constant Summary
collapse
- TITLE =
#
TITLE
Specify which title to use for this small widget.
#
'DNA to Aminoacid Sequence converter'
- WIDTH =
'65% or 500px minimum'
- 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 =
:hack_16
- USE_THIS_SLIGHTLY_SMALLER_FONT =
#
USE_THIS_SLIGHTLY_SMALLER_FONT
#
:hack_16
ARRAY_ALL_GTK_WIDGETS, FONT_SIZE, OLD_VERBOSE_VALUE, Bioroebe::GUI::USE_THIS_FONT_FAMILY_FOR_GUI_APPLICATIONS
ColoursForBase::ARRAY_HTML_COLOURS_IN_USE
Class Method Summary
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Instance Method Summary
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#disable_warnings, #enable_warnings, #log_dir?
#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
#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) ⇒ DnaToAminoacidWidget
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 80
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
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 674
def self.[](i = ARGV)
new(i)
end
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.run(i = ARGV) ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 681
def self.run(
i = ARGV
)
r = ::Gtk.runner_factory(
::Bioroebe::GUI::Gtk::DnaToAminoacidWidget.new(i)
)
r.modify_background(:normal, :mintcream)
return r
end
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Instance Method Details
#assign_this_fasta_file(i) ⇒ Object
#
assign_this_fasta_file
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 577
def assign_this_fasta_file(i)
i = ::Bioroebe.parse_fasta(i).sequence?
i.upcase! if i
set_dna_sequence(i)
end
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#border_size? ⇒ Boolean
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 137
def border_size?
8
end
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 263
def button_trigger_the_conversion?
@button_trigger_conversion
end
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#connect_the_skeleton ⇒ Object
#
connect_the_skeleton (connect tag, skeleton tag)
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 586
def connect_the_skeleton
abort_on_exception
vbox = create_vbox
dna_sequence_label = bold_label('DNA sequence')
dna_sequence_label.set_size_request(sanitized_half_width, 42)
aminoacid_sequence_label = bold_label('Aminoacid sequence')
aminoacid_sequence_label.set_size_request(sanitized_half_width, 42)
@grid.attach(dna_sequence_label, 0, 0, 2, 1)
@grid.attach(aminoacid_sequence_label, 3, 0, 2, 1)
@grid.attach(@left_entry, 0, 1, 2, 1)
@grid.attach(@event_box_containing_the_right_arrow, 2, 1, 1, 1)
@grid.attach(@right_entry, 3, 1, 2, 1)
button_box = simplified_button_box(button_trigger_the_conversion?)
button_box.set_size_request(350, 40)
@grid.attach(
button_box, 0, 2, 5, 1
)
vbox.minimal(@header_bar)
vbox.add(horizontal_spacer)
vbox.minimal(@grid, 8)
vbox.add(horizontal_spacer)
hbox = create_hbox
dropdown_box = gtk_dropdown_box(
Bioroebe.available_codon_tables?
)
dropdown_box.use_this_font = SMALLER_FONT
dropdown_box.first_element_is_active
dropdown_box.bblack1
dropdown_box.pad5px
dropdown_box.hint = 'When a new codon table is assigned, via the '\
'drop-down menu, then any assigned DNA sequence will be automatically '\
'translated to its corresponding amino acid sequence.'
dropdown_box.on_changed {
new_text = dropdown_box.text?.to_s
@entry_for_the_codon_table_in_use.set_text(new_text)
do_determine_the_aminoacid_sequence
}
hbox.minimal(text('Codon table in use:'), 3)
hbox.minimal(@entry_for_the_codon_table_in_use, 3)
hbox.minimal(dropdown_box, 3)
vbox.add(hbox)
@label_n_DNA_nucleotides = bold_label('n DNA nucleotides: ')
@label_n_DNA_nucleotides.align_left
@label_n_DNA_nucleotides.make_selectable
vbox.add(@label_n_DNA_nucleotides)
@label_n_aminoacids = bold_label('n aminoacids: ')
@label_n_aminoacids.align_left
@label_n_aminoacids.make_selectable
vbox.add(@label_n_aminoacids)
window = runner_widget(nil, width?, height?, title?)
window << 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?)
window.set_size_request(80, 100)
window.top_left
run_main
end
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 424
def create_button_trigger_conversion
@button_trigger_conversion = bold_button('_Trigger Conversion')
@button_trigger_conversion.clear_background
@button_trigger_conversion.disallow_resizing
@button_trigger_conversion.set_size_request(125, 40)
@button_trigger_conversion.set_background_colour :whitesmoke
@button_trigger_conversion.on_hover(:lightgreen)
@button_trigger_conversion.on_clicked {
update_the_dna_sequence_then_do_the_conversion
do_properly_space_the_top_left_entry
}
@button_trigger_conversion.bblack2
@button_trigger_conversion.hint =
"Clicking on this button will convert from a <b>DNA</b> "\
"<b>sequence</b> \n(on the left hand side) to the <b>corresponding "\
"Aminoacid sequence</b>.\n\nMake sure you input the DNA sequence "\
"on the left hand side. The space character, aka ' ', will "\
"be ignored."
end
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#create_the_entries ⇒ Object
#
create_the_entries (entries tag)
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 372
def create_the_entries
create_the_left_entry
create_the_right_entry
create_the_entry_for_the_codon_table_in_use
end
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#create_the_entry_for_the_codon_table_in_use ⇒ Object
#
create_the_entry_for_the_codon_table_in_use
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 235
def create_the_entry_for_the_codon_table_in_use
@entry_for_the_codon_table_in_use = create_entry(Bioroebe.codon_table_in_use?.to_s)
@entry_for_the_codon_table_in_use.center
@entry_for_the_codon_table_in_use.bblack2
@entry_for_the_codon_table_in_use.bg_azure
@entry_for_the_codon_table_in_use.read_only
@entry_for_the_codon_table_in_use.use_this_font = SMALLER_FONT
@entry_for_the_codon_table_in_use.width_height(450, 42)
end
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#create_the_event_box ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 251
def create_the_event_box
@event_box_containing_the_right_arrow = create_eventbox(
text(:arrow_right)
)
@event_box_containing_the_right_arrow.on_clicked {
update_the_dna_sequence_then_do_the_conversion
}
end
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#create_the_grid ⇒ Object
#
create_the_grid (grid tag)
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 277
def create_the_grid
@grid = create_grid
@grid.set_column_spacing(5)
@grid.set_row_spacing(5)
end
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 460
def
@header_bar =
@header_bar.pad8px
@header_bar.bblack1
button_open_file = icon_theme(:open_file)
button_open_file.hint = 'Click on this button to open a '\
'local FASTA file.'
button_open_file.on_clicked {
result = do_pick_a_local_file
if result and File.file?(result) and result.end_with?('.fasta','.fa')
assign_this_fasta_file(result)
end
}
@header_bar.pack_left(button_open_file)
end
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#create_the_left_entry ⇒ Object
#
create_the_left_entry (left tag)
This entry will keep the DNA sequence.
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 557
def create_the_left_entry
@left_entry = create_entry
@left_entry.clear_background
@left_entry.yellow_background
@left_entry.bblack1
@left_entry.pad5px
@left_entry.set_size_request(sanitized_half_width, 42)
@left_entry.hint = 'You can either hit the enter key here, or '\
'click the trigger-conversion button.'
@left_entry.on_enter_key {
update_the_dna_sequence_then_do_the_conversion
}
end
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#create_the_right_entry ⇒ Object
#
create_the_right_entry
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 345
def create_the_right_entry
@right_entry = create_entry
@right_entry.clear_background
@right_entry.lightskyblue_background
@right_entry.bblack1
@right_entry.pad5px
@right_entry.set_size_request(sanitized_half_width, 42)
end
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#create_the_skeleton ⇒ Object
#
create_the_skeleton (create tag, skeleton tag)
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 413
def create_the_skeleton
create_the_grid
create_button_trigger_conversion
create_the_entries
create_the_event_box
end
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#dna_sequence? ⇒ Boolean
Also known as:
return_the_main_DNA_sequence
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 365
def dna_sequence?
left_entry?.text.to_s
end
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#do_pick_a_local_file ⇒ Object
#
do_pick_a_local_file (open tag)
This method is run when the user wants to open a local file.
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 481
def do_pick_a_local_file
create_a_new_file_chooser_dialog(self) {{
start_dir: return_pwd,
show_hidden_files: :yes,
current_folder: ::Bioroebe.log_dir?,
additional_directories: [
::Bioroebe.log_dir?,
ENV['PC'].to_s,
ENV['MY_TEMP'].to_s,
ENV['RSRC'].to_s
]
}}
_ = ::Gtk.main_file?.to_s
return _
end
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#do_properly_space_the_top_left_entry ⇒ Object
#
do_properly_space_the_top_left_entry
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 303
def do_properly_space_the_top_left_entry
old_text = @left_entry.text?.delete(' ')
_ = old_text.
gsub(/(.{3})/,' \1').
lstrip
@left_entry.set_text(_)
end
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#do_the_conversion(i = @dna_sequence) ⇒ Object
Also known as:
do_sync_fields, do_trigger_the_conversion, do_determine_the_aminoacid_sequence
#
do_the_conversion (conversion tag)
This is the method that is to be used for the actual conversion.
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 187
def do_the_conversion(
i = @dna_sequence
)
sanitized_input = i.delete(' ').delete('-')
i.tr!('U','T') if i.include? 'U'
set_dna_sequence(i)
if ::Bioroebe.const_defined? :Controller
::Bioroebe::GUI::Controller.set_dna_sequence(i)
end
aminoacid_sequence = ::Bioroebe.convert_dna_to_protein_sequence(
sanitized_input,
:default,
Bioroebe::CodonTable.by_name(
entry_for_the_codon_table?.text?
)
)
set_aminoacid_sequence(aminoacid_sequence)
update_the_entries
sync_the_entries_back_onto_the_two_main_strings
if @parent_widget and @parent_widget.respond_to?(:set_aminoacid_sequence)
@parent_widget.set_aminoacid_sequence(aminoacid_sequence)
end
@label_n_DNA_nucleotides.set_text(
'n DNA nucleotides: '+
i.delete(' ').
delete('-').size.to_s
)
@label_n_DNA_nucleotides.make_bold
@label_n_DNA_nucleotides.align_left
@label_n_aminoacids.set_text(
'n aminoacids: '+
aminoacid_sequence.size.to_s
)
@label_n_aminoacids.make_bold
@label_n_aminoacids.align_left
end
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#entry_for_the_codon_table? ⇒ Boolean
#
entry_for_the_codon_table?
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 314
def entry_for_the_codon_table?
@entry_for_the_codon_table_in_use
end
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#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/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 395
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_rules
end
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#left_entry? ⇒ Boolean
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 296
def left_entry?
@left_entry
end
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#main_font? ⇒ Boolean
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 381
def main_font?
USE_THIS_FONT
end
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 519
def (
i = commandline_arguments?
)
if i and i.is_a?(Array)
if i.empty?
set_dna_sequence(:default)
update_the_left_entry
else
i.each {|entry| (entry) }
end
else
case i when 'ubiquitin',
'ubi'
i = ''
set_these_aminoacids(
::Bioroebe.return_ubiquitin_sequence
)
else
assign_this_fasta_file(i)
update_the_left_entry
end
end
end
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#padding? ⇒ Boolean
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 130
def padding?
8
end
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#reset ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 95
def reset
super() if respond_to?(:super)
reset_the_internal_variables
reset_the_base_module infer_the_namespace
@configuration = [true, __dir__, namespace?]
title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
handle_CSS if use_gtk3?
@dna_sequence = :default
@aminoacid_sequence = ''.dup
@parent_widget = nil
end
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#right_entry? ⇒ Boolean
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 321
def right_entry?
@right_entry
end
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#run ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 453
def run
run_super
end
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#sanitized_half_width ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 289
def sanitized_half_width
(width? / 2.to_f) - 30
end
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#set_aminoacid_sequence(i) ⇒ Object
Also known as:
set_these_aminoacids
#
set_aminoacid_sequence
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 178
def set_aminoacid_sequence(i)
@aminoacid_sequence = i
end
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#set_dna_sequence(i = left_entry?.text) ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 500
def set_dna_sequence(
i = left_entry?.text
)
case i
when :default
i = 'ATG CGG'.dup
end
if i and i.start_with?('--')
i = '' end
@dna_sequence = i.to_s.dup
end
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#set_left_entry(i = @dna_sequence) ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 161
def set_left_entry(
i = @dna_sequence
)
left_entry?.set_text(i)
end
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 328
def set_parent_widget(i)
@parent_widget = i
end
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#set_right_entry(i = @aminoacid_sequence) ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 152
def set_right_entry(
i = @aminoacid_sequence
)
right_entry?.set_text(i)
end
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#slightly_smaller_font? ⇒ Boolean
#
slightly_smaller_font?
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 388
def slightly_smaller_font?
USE_THIS_SLIGHTLY_SMALLER_FONT
end
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#sync_the_entries_back_onto_the_two_main_strings ⇒ Object
#
sync_the_entries_back_onto_the_two_main_strings
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 170
def sync_the_entries_back_onto_the_two_main_strings
@dna_sequence = return_the_main_DNA_sequence
@aminoacid_sequence = right_entry?.text.to_s
end
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#update_the_dna_sequence_then_do_the_conversion ⇒ Object
#
update_the_dna_sequence_then_do_the_conversion
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 335
def update_the_dna_sequence_then_do_the_conversion
set_dna_sequence(
left_entry?.text.upcase )
do_the_conversion
end
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#update_the_entries ⇒ Object
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 144
def update_the_entries
set_left_entry
set_right_entry
end
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#update_the_left_entry ⇒ Object
#
update_the_left_entry
#
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# File 'lib/bioroebe/gui/universal_widgets/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb', line 270
def update_the_left_entry
set_left_entry(@dna_sequence.to_s)
end
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