bioroebe 0.10.80

data/lib/bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb

@@ -0,0 +1,609 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::DnaToAminoacidWidget
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/dna_to_aminoacid_widget/dna_to_aminoacid_widget.rb'
+# Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class DnaToAminoacidWidget < ::Gtk::Box # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget 
+
+  require 'bioroebe/constants/GUIs.rb'
+  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/toplevel_methods/misc.rb'
+  require 'bioroebe/fasta_and_fastq/parse_fasta/parse_fasta.rb'
+  require 'bioroebe/codons/codons.rb'
+  require 'bioroebe/codons/codon_table.rb'
+  require 'bioroebe/codons/show_codon_tables.rb'
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'DNA to Aminoacid Sequence converter'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH  = '80%'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '35% or minimum 120px'
+
+  # ========================================================================= #
+  # === MAIN_FONT
+  # ========================================================================= #
+  MAIN_FONT = :dejavu_condensed_16
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :dejavu_condensed_14
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    super(:vertical)
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  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(15) if respond_to? :set_border_width
+    signal_destroy_then_quit
+    # ======================================================================= #
+    # === @dna_sequence
+    #
+    # This is the dna sequence we will use. We will not work on the
+    # entry directly, as this depends on gtk-initialization which
+    # may not yet have happened.
+    # ======================================================================= #
+    @dna_sequence = :default
+    # ======================================================================= #
+    # === @aminoacid_sequence
+    # ======================================================================= #
+    @aminoacid_sequence = ''.dup
+    # ======================================================================= #
+    # === @parent_widget
+    # ======================================================================= #
+    @parent_widget = nil
+    handle_CSS_rules
+  end
+
+  # ========================================================================= #
+  # === handle_CSS_rules
+  # ========================================================================= #
+  def handle_CSS_rules
+    use_gtk_paradise_project_css_file
+    append_project_CSS_file 
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    8
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    4
+  end
+
+  # ========================================================================= #
+  # === update_the_entries
+  # ========================================================================= #
+  def update_the_entries
+    set_left_entry
+    set_right_entry
+  end
+
+  # ========================================================================= #
+  # === set_right_entry
+  # ========================================================================= #
+  def set_right_entry(
+      i = @aminoacid_sequence
+    )
+    right_entry?.set_text(i)
+  end
+
+  # ========================================================================= #
+  # === set_left_entry
+  # ========================================================================= #
+  def set_left_entry(
+      i = @dna_sequence
+    )
+    left_entry?.set_text(i)
+  end
+
+  # ========================================================================= #
+  # === sync_the_entries_back_onto_the_two_main_strings
+  # ========================================================================= #
+  def sync_the_entries_back_onto_the_two_main_strings
+    @dna_sequence       = left_entry?.text.to_s
+    @aminoacid_sequence = right_entry?.text.to_s
+  end
+
+  # ========================================================================= #
+  # === create_the_entries                                      (entries tag)
+  # ========================================================================= #
+  def create_the_entries
+    create_the_left_entry
+    create_the_right_entry
+    create_the_entry_for_the_codon_table_in_use
+  end
+
+  # ========================================================================= #
+  # === create_the_entry_for_the_codon_table_in_use
+  # ========================================================================= #
+  def create_the_entry_for_the_codon_table_in_use
+    # ======================================================================= #
+    # === @entry_for_the_codon_table_in_use
+    # ======================================================================= #
+    @entry_for_the_codon_table_in_use = gtk_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
+
+  # ========================================================================= #
+  # === create_the_event_box
+  # ========================================================================= #
+  def create_the_event_box
+    @event_box_containing_the_right_arrow = gtk_eventbox(
+      gtk_label(:arrow_right)
+    )
+    @event_box_containing_the_right_arrow.on_clicked {
+      update_the_dna_sequence_then_do_the_conversion
+    }
+  end
+
+  # ========================================================================= #
+  # === button_trigger_the_conversion?
+  # ========================================================================= #
+  def button_trigger_the_conversion?
+    @button_trigger_conversion
+  end
+
+  # ========================================================================= #
+  # === update_the_left_entry
+  # ========================================================================= #
+  def update_the_left_entry
+    set_left_entry(@dna_sequence.to_s)
+  end
+
+  # ========================================================================= #
+  # === create_grid                                                (grid tag)
+  # ========================================================================= #
+  def create_grid
+    # ======================================================================= #
+    # === @grid
+    # ======================================================================= #
+    @grid = gtk_grid
+    @grid.set_column_spacing(5)
+    @grid.set_row_spacing(5)
+  end
+
+  # ========================================================================= #
+  # === sanitized_half_width
+  # ========================================================================= #
+  def sanitized_half_width
+    (@width / 2)- 30
+  end
+
+  # ========================================================================= #
+  # === left_entry?
+  # ========================================================================= #
+  def left_entry?
+    @left_entry
+  end
+
+  # ========================================================================= #
+  # === entry_for_the_codon_table?
+  # ========================================================================= #
+  def entry_for_the_codon_table?
+    @entry_for_the_codon_table_in_use
+  end
+
+  # ========================================================================= #
+  # === right_entry?
+  # ========================================================================= #
+  def right_entry?
+    @right_entry
+  end
+
+  # ========================================================================= #
+  # === set_parent_widget
+  # ========================================================================= #
+  def set_parent_widget(i)
+    @parent_widget = i
+  end
+
+  # ========================================================================= #
+  # === update_the_dna_sequence_then_do_the_conversion
+  # ========================================================================= #
+  def update_the_dna_sequence_then_do_the_conversion
+    set_dna_sequence(
+      left_entry?.text
+    )
+    do_the_conversion
+  end
+
+  # ========================================================================= #
+  # === create_the_right_entry
+  # ========================================================================= #
+  def create_the_right_entry
+    # ======================================================================= #
+    # === The right Aminoacid widget.
+    # ======================================================================= #
+    @right_entry = gtk_entry
+    @right_entry.clear_background
+    @right_entry.lightskyblue_background
+    @right_entry.bblack1
+    @right_entry.pad5px
+    @right_entry.set_size_request(sanitized_half_width, 42)
+    # ======================================================================= #
+    # The AA widget. Will be highlighted on a click event. This was
+    # reconsidered and disabled as of August 2021.
+    # ======================================================================= #
+    # @right_entry.on_click_event { :select_text }
+  end
+
+  # ========================================================================= #
+  # === create_button_trigger_conversion
+  # ========================================================================= #
+  def create_button_trigger_conversion
+    # ======================================================================= #
+    # === @button_trigger_conversion
+    # ======================================================================= #
+    @button_trigger_conversion = gtk_bold_button('_Trigger Conversion')
+    @button_trigger_conversion.disallow_resizing
+    @button_trigger_conversion.set_size_request(125, 40)
+    @button_trigger_conversion.lightgreen
+    @button_trigger_conversion.set_background_colour :whitesmoke
+    @button_trigger_conversion.on_clicked {
+      update_the_dna_sequence_then_do_the_conversion
+    }
+    @button_trigger_conversion.bblack2
+    # ======================================================================= #
+    # Use a tooltip as well for our button:
+    # ======================================================================= #
+    @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
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    # ======================================================================= #
+    # The two top labels denote which widget is the one for the DNA
+    # sequence, and which one is for the aminoacid sequence.
+    # ======================================================================= #
+    dna_sequence_label       = gtk_bold_label('DNA sequence')
+    dna_sequence_label.set_size_request(sanitized_half_width, 42)
+    aminoacid_sequence_label = gtk_bold_label('Aminoacid sequence')
+    aminoacid_sequence_label.set_size_request(sanitized_half_width, 42)
+    # ======================================================================= #
+    # API for .attach() is:
+    #   .attach(child, left, top, width, height)
+    # ======================================================================= #
+    @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
+    )
+    minimal(@header_bar)
+    add(horizontal_spacer)
+    minimal(@grid, 8)
+    add(horizontal_spacer)
+    hbox = gtk_hbox
+    # ======================================================================= #
+    # Add the dropdown box next; also known as the combobox.
+    # ======================================================================= #
+    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.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)
+    add(hbox)
+    vbox = gtk_vbox
+    @label_n_DNA_nucleotides = gtk_bold_label('n DNA nucleotides: ')
+    @label_n_DNA_nucleotides.align_left
+    vbox.add(@label_n_DNA_nucleotides)
+    @label_n_aminoacids = gtk_bold_label('n aminoacids:      ')
+    @label_n_aminoacids.align_left
+    vbox.add(@label_n_aminoacids)
+    minimal(vbox)
+  end
+
+  # ========================================================================= #
+  # === create_the_header_bar
+  # ========================================================================= #
+  def create_the_header_bar
+    @header_bar = return_default_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
+
+  # ========================================================================= #
+  # === do_pick_a_local_file                                       (open tag)
+  #
+  # This method is run when the user wants to open a local file.
+  # ========================================================================= #
+  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'],
+        ENV['MY_TEMP'],
+        ENV['RSRC']
+      ]
+    }}
+    _ = ::Gtk.main_file?.to_s
+    return _
+  end
+
+  # ========================================================================= #
+  # === set_dna_sequence
+  # ========================================================================= #
+  def set_dna_sequence(
+      i = left_entry?.text
+    )
+    case i
+    # ======================================================================= #
+    # === :default
+    # ======================================================================= #
+    when :default
+      i = 'ATG CGG'.dup
+    end
+    if i and i.start_with?('--')
+      i = '' # Ad-hoc fix.
+    end
+    @dna_sequence = i.to_s.dup
+  end
+
+  # ========================================================================= #
+  # === menu                                                       (menu tag)
+  # ========================================================================= #
+  def menu(
+      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| menu(entry) }
+      end
+    else
+      case i # Perform some sanitizing here. (case tag)
+      # ===================================================================== #
+      # === ubiquitin
+      # ===================================================================== #
+      when 'ubiquitin',
+           'ubi'
+        i = ''
+        set_these_aminoacids(
+          ::Bioroebe.return_ubiquitin_sequence
+        )
+      else
+        # =================================================================== #
+        # Else we will simply assign the DNA sequence as-is. If the input
+        # is a .fasta or .fasta file then we will use ParseFasta to obtain
+        # the real sequence instead.
+        # =================================================================== #
+        assign_this_fasta_file(i)
+        update_the_left_entry
+      end
+    end
+  end
+
+  # ========================================================================= #
+  # === create_the_left_entry                                      (left tag)
+  #
+  # This entry will keep the DNA sequence.
+  # ========================================================================= #
+  def create_the_left_entry
+    # ======================================================================= #
+    # The left entry, a DNA widget as a gtk-entry widget.
+    # ======================================================================= #
+    @left_entry = gtk_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
+
+  # ========================================================================= #
+  # === assign_this_fasta_file
+  # ========================================================================= #
+  def assign_this_fasta_file(i)
+    i = ::Bioroebe.parse_fasta(i).sequence?
+    i.upcase! if i
+    set_dna_sequence(i)
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_header_bar
+    create_grid
+    create_button_trigger_conversion
+    create_the_entries
+    create_the_event_box
+  end
+
+  # ========================================================================= #
+  # === set_aminoacid_sequence
+  # ========================================================================= #
+  def set_aminoacid_sequence(i)
+    @aminoacid_sequence = i
+  end; alias set_these_aminoacids set_aminoacid_sequence # === set_these_aminoacids
+
+  # ========================================================================= #
+  # === do_the_conversion                                    (conversion tag)
+  #
+  # This is the method that is to be used for the actual conversion.
+  # ========================================================================= #
+  def do_the_conversion(
+      i = @dna_sequence
+    )
+    # ======================================================================= #
+    # Next, we must translate from DNA to Aminoacid sequence.
+    # ======================================================================= #
+    sanitized_input = i.delete(' ').delete('-')
+    i.tr!('U','T') if i.include? 'U'
+    set_dna_sequence(i)
+    if ::Bioroebe.const_defined? :Controller
+      # ===================================================================== #
+      # Ok, in this case we can store the dataset via a class-method.
+      # ===================================================================== #
+      ::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; alias do_sync_fields                      do_the_conversion # === do_sync_fields
+       alias do_trigger_the_conversion           do_the_conversion # === do_trigger_the_conversion
+       alias do_determine_the_aminoacid_sequence do_the_conversion # === do_determine_the_aminoacid_sequence
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    super()
+    menu
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget[]
+  # ========================================================================= #
+  def self.[](i = '')
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::DnaToAminoacidWidget.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic_size_then_automatic_title
+    r.top_left_then_run
+  end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run_gtk3_widget
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::DnaToAminoacidWidget.run
+end # gtkdnatoaminoacidwidget

data/lib/bioroebe/gui/gtk3/dna_to_reverse_complement_widget/dna_to_reverse_complement_widget.config

@@ -0,0 +1,6 @@
+width:                                      1300
+height:                                      220
+padding:                                       4
+title:                 DNA to reverse complement
+favicon:                                 :tabble
+font_in_use:                             Sans 22