bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/libui/random_sequence/random_sequence.rb

@@ -1,190 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::RandomSequence
-# =========================================================================== #
-# require 'bioroebe/gui/libui/random_sequence/random_sequence.rb' 
-# =========================================================================== #
-require 'bioroebe/constants/GUIs.rb'
-
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
-
-  require 'bioroebe/count/count_amount_of_aminoacids.rb'
-
-  require 'libui_paradise'
-  include LibuiParadise::Extensions
-  
-  require 'bioroebe/sequence/sequence.rb'
-  require 'bioroebe/aminoacids/create_random_aminoacids.rb'
-  require 'bioroebe/toplevel_methods/misc.rb'
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Random Sequence - for DNA, RNA and aminoacids'
-
-  # ========================================================================= #
-  # === HEIGHT
-  # ========================================================================= #
-  HEIGHT = 500
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize
-    reset
-  end
-
-  # ========================================================================= #
-  # === reset_then_run
-  # ========================================================================= #
-  def reset_then_run
-    reset
-    run
-  end
-
-  # ========================================================================= #
-  # === reset
-  # ========================================================================= #
-  def reset
-  end
-
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    create_the_entries
-    # ======================================================================= #
-    # === @text_buffer
-    # ======================================================================= #
-    @text_buffer = ui_text_view
-  end
-
-  # ========================================================================= #
-  # === create_the_entries
-  # ========================================================================= #
-  def create_the_entries
-    # ======================================================================= #
-    # === @entry_containing_the_sequence
-    # ======================================================================= #
-    @entry_containing_the_sequence = ui_entry
-    # ======================================================================= #
-    # === @entry_use_this_length
-    # ======================================================================= #
-    @entry_use_this_length = ui_entry(15)
-  end
-
-  # ========================================================================= #
-  # === aminoacid_sequence?
-  # ========================================================================= #
-  def aminoacid_sequence?
-    @entry_containing_the_sequence.text?.to_s
-  end; alias sequence?      aminoacid_sequence? # === sequence?
-       alias main_sequence? aminoacid_sequence? # === main_sequence?
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    create_skeleton
-    main_window = ui_margined_window(TITLE, 1200, HEIGHT, 15)
-    outer_vbox = ui_padded_vbox
-    outer_vbox.minimal(@entry_containing_the_sequence)
-    button_generate_a_random_aminoacid_sequence = ui_button(
-      'Generate a random aminoacid sequence'
-    )
-    button_generate_a_random_aminoacid_sequence.on_clicked {
-      do_generate_a_random_sequence(n_aminoacids?)
-    }
-    outer_vbox.minimal(button_generate_a_random_aminoacid_sequence)
-    outer_vbox.minimal(@entry_use_this_length)
-    outer_vbox.minimal(
-      ui_text(
-        'Showing statistical information about the '\
-        'assigned aminoacid sequence next'
-      )
-    )
-    outer_vbox.maximal(@text_buffer)
-    main_window.child = outer_vbox
-    main_window.intelligent_exit
-  end
-
-  # ========================================================================= #
-  # === do_generate_a_random_sequence_using_the_value_from_the_proper_entry
-  #
-  # This variant will be guaranteed to use the value determined by the
-  # gtk entry.
-  # ========================================================================= #
-  def do_generate_a_random_sequence_using_the_value_from_the_proper_entry(
-      i = n_aminoacids?
-    )
-    i = i.to_i
-    if i > 5_000_000
-      i = 5_000_000
-      set_main_entry(i.to_s)
-    end
-    do_generate_a_random_sequence(i)
-  end
-
-  # ========================================================================= #
-  # === do_generate_a_random_sequence
-  # ========================================================================= #
-  def do_generate_a_random_sequence(
-      n_aminoacids = :default
-    )
-    case n_aminoacids
-    when nil, :default
-      n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
-    end
-    n_aminoacids = n_aminoacids.to_i
-    if n_aminoacids > 5_000_000
-      n_aminoacids = 5_000_000
-      set_main_entry(n_aminoacids.to_s)
-    end
-    use_this_as_the_new_sequence = ::Bioroebe.create_random_aminoacids(n_aminoacids).to_s
-    array1 = ::Bioroebe.return_array_of_common_aminoacids
-    array2 = Bioroebe::CountAmountOfAminoacids.return_composition_hash(use_this_as_the_new_sequence).values.map(&:to_s)
-    zipped = array1.zip(array2) # Zip it up with 0-values here.
-    _ = ''.dup
-    zipped.each {|a, b|
-      _ << "#{a}: #{b}\n"
-    }
-    @text_buffer.set_text(_)
-    @entry_containing_the_sequence.set_text(use_this_as_the_new_sequence)
-  end
-
-  # ========================================================================= #
-  # === n_aminoacids?
-  # ========================================================================= #
-  def n_aminoacids?
-    @entry_use_this_length.text?.to_s
-  end
-
-  # ========================================================================= #
-  # === set_main_entry
-  # ========================================================================= #
-  def set_main_entry(i)
-    @entry_use_this_length.set_text(i.to_s)
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::LibUI::RandomSequence.run
-  # ========================================================================= #
-  def self.run
-    object = Object.new.dup
-    object.extend(RandomSequence)
-    object.reset_then_run
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::RandomSequence.run
-end

data/lib/bioroebe/gui/libui/show_codon_table/show_codon_table.rb

@@ -1,134 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::ShowCodonTable
-# =========================================================================== #
-# require 'bioroebe/gui/libui/show_codon_table/show_codon_table.rb'
-# =========================================================================== #
-require 'bioroebe/constants/GUIs.rb'
-
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-module ShowCodonTable # === Bioroebe::GUI::LibUI::ShowCodonTable
-
-  require 'libui_paradise'
-  include LibuiParadise::Extensions
-
-  require 'bioroebe/codons/codon_tables.rb'
-
-  require 'bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb'
-  include Bioroebe::GUI::ShowCodonTableModule
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Show Codon Table'
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize
-    reset
-  end
-
-  # ========================================================================= #
-  # === reset_then_run
-  # ========================================================================= #
-  def reset_then_run
-    reset
-    run
-  end
-
-  # ========================================================================= #
-  # === reset
-  # ========================================================================= #
-  def reset
-    reset_the_shared_module
-  end
-    
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    create_the_combo_box
-  end
-
-  # ========================================================================= #
-  # === create_the_combo_box
-  # ========================================================================= #
-  def create_the_combo_box
-    @combo_box_containing_the_registered_codon_tables = ui_combobox
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    create_skeleton
-    hash = ::Bioroebe.hash_codon_tables?
-    values = hash.values
-    main_window = margined_window(TITLE, 1200, 200, 0)
-    @toplabel = text(values.first.to_s)
-
-    # combobox_selected_callback = proc { |pointer_to_index|
-    #   index = UI.combobox_selected(pointer_to_index)
-    #  selected_text = values[index].to_s
-    #   main_hash?[
-    #     @toplabel.object_id
-    #   ].first..set_text(selected_text)
-    # }
-
-    outer_vbox    = padded_vbox
-    toplevel_hbox = padded_hbox
-
-    toplevel_hbox.maximal(@toplabel)
-    outer_vbox << toplevel_hbox
-    @text_buffer = text_view
-    outer_vbox << @text_buffer
-    hbox = padded_hbox
-    _ = text('Select the codon table (default: eukaryotes) → ')
-    hbox.minimal(_)
-    create_the_combo_box
-
-    combobox_selected_callback = proc {|pointer|
-      e 'The active text was: '+active_text?
-    }
-    UI.combobox_on_selected(
-      @combo_box_containing_the_registered_codon_tables,
-      combobox_selected_callback,
-      nil
-    )
-    @combo_box_containing_the_registered_codon_tables.append_this_array(hash.values)
-    hbox.maximal(
-      @combo_box_containing_the_registered_codon_tables
-    )
-    outer_vbox << hbox
-    @button_do_analyse = button('Do Analyse')
-    @button_do_analyse.on_clicked {
-e 'clicked'
-    }
-
-    outer_vbox << @button_do_analyse
-    main_window.child = outer_vbox
-    main_window.complex_finalizer
-  end
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::LibUI::ShowCodonTable.run
-  # ========================================================================= #
-  def self.run
-    object = Object.new
-    object.extend(ShowCodonTable)
-    object.reset_then_run
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::ShowCodonTable.run
-end

data/lib/bioroebe/gui/libui/show_codon_usage/show_codon_usage.rb

@@ -1,89 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::ShowCodonUsage
-# =========================================================================== #
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-class ShowCodonUsage # === Bioroebe::GUI::LibUI::ShowCodonUsage
-
-  require 'libui_paradise'
-  include LibuiParadise::Extensions
-
-  require 'bioroebe/gui/shared_code/show_codon_usage/show_codon_usage_module.rb'
-  include Bioroebe::GUI::ShowCodonUsageModule
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize(
-      run_already = true
-    )
-    reset
-    run if run_already
-  end
-
-  # ========================================================================= #
-  # === reset                                                     (reset tag)
-  # ========================================================================= #
-  def reset
-    reset_the_shared_module
-  end
-
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    create_the_main_entry
-    create_the_label_top_five_codons
-    create_the_label_showing_n_nucleotides
-    create_box_top_five_codons
-    create_the_text_view
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    create_skeleton
-    window = ui_padded_main_window(
-      TITLE,
-      WIDTH,
-      HEIGHT,
-      0
-    )
- 
-    outer_vbox = padded_vbox
-    mini_hbox = hbox
-    mini_hbox.maximal(@entry1)
-    button_do_the_conversion = button('Do the conversion')
-    button_do_the_conversion.on_clicked {
-      do_the_conversion_then_update_the_label_as_well
-    }
-    mini_hbox.minimal(button_do_the_conversion)
-    outer_vbox.minimal(mini_hbox)
-    outer_vbox.add_hsep
-    outer_vbox.minimal(@label_showing_n_nucleotides)
-    outer_vbox.add_hsep
-    mini_hbox = hbox
-    @box_top_five_codons.minimal(@label_top_five_codons, 10)
-    mini_hbox.maximal(@text_view)
-    mini_hbox.maximal(@box_top_five_codons)
-    outer_vbox.maximal(mini_hbox)
-    outer_vbox.add_hsep
-    button_quit = quit_button
-    outer_vbox.minimal(button_quit)
-    window.add(outer_vbox)
-    window.intelligent_exit
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::ShowCodonUsage.new  
-end

data/lib/bioroebe/gui/libui/three_to_one/three_to_one.rb

@@ -1,113 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::LibUI::ThreeToOne
-# =========================================================================== #
-require 'bioroebe/constants/GUIs.rb'
-
-module Bioroebe
-
-module GUI
-
-module LibUI
-
-module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
-
-  require 'libui_paradise/autoinclude'
-  include LibuiParadise::Extensions
-
-  require 'bioroebe/gui/gtk3/three_to_one/title.rb'
-  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = ::Bioroebe::GUI::Gtk::ThreeToOneModule::TITLE
-
-  # ========================================================================= #
-  # === initialize
-  # ========================================================================= #
-  def initialize
-  end
-
-  # ========================================================================= #
-  # === create_skeleton                                          (create tag)
-  # ========================================================================= #
-  def create_skeleton
-    @entry1 = entry
-    @entry2 = entry
-    @checkbox1 = checked_checkbox
-    @checkbox2 = checkbox
-  end
-
-  # ========================================================================= #
-  # === run
-  # ========================================================================= #
-  def run
-    create_skeleton
-    main_window = ui_margined_window(TITLE, 1200, 200, 15)
-    outer_vbox = ui_vbox
-
-    top_hbox = ui_hbox
-    top_hbox << ui_text('Input sequence:')
-    outer_vbox << top_hbox
-    outer_vbox << @entry1
-    outer_vbox << @entry2
-    bottom_hbox = ui_hbox
-    convert_button = ui_button('Convert')
-    convert_button.on_clicked {
-      do_the_conversion
-    }
-    bottom_hbox << convert_button
-    vbox_with_checkbuttons = ui_vbox
-
-    small_hbox1 = ui_hbox
-    small_hbox1 << ui_text('3-to-1 conversion')
-    small_hbox1 << @checkbox1
-    vbox_with_checkbuttons << small_hbox1
-
-    small_hbox2 = ui_hbox
-    small_hbox2 << ui_text('1-to-3 conversion')
-    small_hbox2 << @checkbox2
-    vbox_with_checkbuttons << small_hbox2
-    vbox_with_checkbuttons << quit_button
-    bottom_hbox << vbox_with_checkbuttons
-    outer_vbox << bottom_hbox
-    main_window.child = outer_vbox
-    main_window.complex_finalizer
-  end
-
-  # ========================================================================= #
-  # === do_trigger_the_conversion                            (conversion tag)
-  # ========================================================================= #
-  def do_trigger_the_conversion(
-      i         = @entry1.text?,
-      checkbox1 = @checkbox1
-    )
-    i = i.to_s.dup.delete(' ')
-    if checkbox1.is_active?
-      new_result = Bioroebe.three_to_one(i).to_s
-    else
-      new_result = Bioroebe.one_to_three(i.delete('-')).to_s
-    end
-    if new_result and new_result.empty?
-      error_msg('No result found. Is it a three-letter aminoacid?')
-    end
-    @entry2.set_text(new_result) if new_result and !new_result.empty?
-  end; alias do_the_conversion do_trigger_the_conversion # === do_the_conversion
-
-  # ========================================================================= #
-  # === Bioroebe::GUI::LibUI::ThreeToOne.run
-  # ========================================================================= #
-  def self.run
-    object = Object.new
-    object.extend(ThreeToOne)
-    object.run
-  end
-
-end; end; end; end
-
-if __FILE__ == $PROGRAM_NAME
-  Bioroebe::GUI::LibUI::ThreeToOne.run
-end

data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb

@@ -1,102 +0,0 @@
-#!/usr/bin/ruby -w
-# Encoding: UTF-8
-# frozen_string_literal: true
-# =========================================================================== #
-# === Bioroebe::GUI::AlignmentModule
-#
-# Usage example:
-#
-#   Alignment.new(ARGV)
-#
-# =========================================================================== #
-# require 'bioroebe/gui/shared_code/alignment/alignment_module.rb'
-# include Bioroebe::GUI::AlignmentModule
-# =========================================================================== #
-module Bioroebe
-
-module GUI
-
-module AlignmentModule # === Bioroebe::GUI::AlignmentModule
-
-  require 'colours'
-  require 'bioroebe/sequence/alignment.rb'
-
-  # ========================================================================= #
-  # === TITLE
-  # ========================================================================= #
-  TITLE = 'Alignment'
-
-  # ========================================================================= #
-  # === TEXT_INPUT_THE_SEQUENCES
-  # ========================================================================= #
-  TEXT_INPUT_THE_SEQUENCES = 'Input the sequences that you wish '\
-                             'to compare to one another'
-
-  # ========================================================================= #
-  # === WIDTH
-  # ========================================================================= #
-  WIDTH = '35% or 300px minimum'
-
-  # ========================================================================= #
-  # === HEIGHT
-  # ========================================================================= #
-  HEIGHT = '45% or 200px minimum'
-
-  # ========================================================================= #
-  # === USE_THIS_FONT
-  # ========================================================================= #
-  USE_THIS_FONT = :dejavu_condensed_20
-
-  # ========================================================================= #
-  # === FONT_FOR_THE_ENTRIES
-  #
-  # The entries must use a mono-spaced font.
-  # ========================================================================= #
-  FONT_FOR_THE_ENTRIES = :hack_20
-
-  # ========================================================================= #
-  # === reset_the_alignment_object
-  # ========================================================================= #
-  def reset_the_alignment_object
-    # ======================================================================= #
-    # === @alignment
-    # ======================================================================= #
-    @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
-  end
-
-  # ========================================================================= #
-  # === return_the_consensus_sequence
-  # ========================================================================= #
-  def return_the_consensus_sequence
-    @alignment.consensus_sequence?
-  end
-
-  # ========================================================================= #
-  # === text_view_widget?
-  # ========================================================================= #
-  def text_view_widget?
-    @text_view
-  end
-
-  # ========================================================================= #
-  # === realign_the_numbers_showing_how_long_the_consensus_sequence_is
-  # ========================================================================= #
-  def realign_the_numbers_showing_how_long_the_consensus_sequence_is
-    @entry_numbers.center if @entry_numbers.respond_to?(:center)
-    n_characters = @entry_consensus_sequence.text?.size
-    @entry_numbers.set_text(return_fill_up_to(n_characters))
-  end
-
-  # ========================================================================= #
-  # === return_fill_up_to
-  # ========================================================================= #
-  def return_fill_up_to(i)
-    _ = ''.dup
-    i.times {|counter|
-      counter = (counter+1) % 10
-      _ << counter.to_s
-    }
-    return _
-  end
-
-end; end; end