bioroebe 0.10.80

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

@@ -0,0 +1,89 @@
+#!/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

@@ -0,0 +1,111 @@
+#!/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 = ui_entry
+    @entry2 = ui_entry
+    @checkbox1 = ui_checkbox
+    @checkbox1.is_active
+    @checkbox2 = ui_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
+
+    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
+    @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/blosum_matrix_viewer/blosum_matrix_viewer_module.rb

@@ -0,0 +1,42 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/blosum_matrix_viewer/blosum_matrix_viewer_module.rb'
+# include Bioroebe::GUI::BlosumMatrixViewerModule
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module BlosumMatrixViewerModule
+
+  require 'bioroebe/blosum/blosum.rb'
+  require 'bioroebe/parsers/blosum_parser.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Blosum Matrix Viewer'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '65% or minimum 650px'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '55% or minimum 500px'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_20
+
+  # ========================================================================= #
+  # === TEXT1
+  # ========================================================================= #
+  TEXT1 = 'Available BLOSUM matrices:'
+
+end; end; end

data/lib/bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb

@@ -0,0 +1,216 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::CalculateCellNumbersOfBacteriaModule
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/calculate_cell_numbers_of_bacteria/calculate_cell_numbers_of_bacteria_module.rb'
+# include Bioroebe::GUI::CalculateCellNumbersOfBacteriaModule
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module CalculateCellNumbersOfBacteriaModule # === Bioroebe::GUI::CalculateCellNumbersOfBacteriaModule 
+
+  require 'bioroebe/toplevel_methods/exponential_growth.rb'
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
+
+  alias e puts
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Calculate cell numbers of bacteria'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH  = '25% or minimum 300px'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '20%'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_20
+
+  # ========================================================================= #
+  # === reset_shared_module
+  # ========================================================================= #
+  def reset_shared_module
+    title_width_height(TITLE, WIDTH, HEIGHT)
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    12
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    4
+  end
+
+  # ========================================================================= #
+  # === do_the_calculation
+  #
+  # This method will do the actual calculation part.
+  # ========================================================================= #
+  def do_the_calculation
+    result = ::Bioroebe.calculate_exponential_growth(
+      number_of_cells     = @entry_point_start_with_n_bacteria.text?,
+      number_of_divisions = @entry_point_use_n_divisions.text?
+    )
+    @entry_point_n_cells.set_text(result.to_s)
+  end
+
+  # ========================================================================= #
+  # === create_the_button_to_calculate_how_many_bacteria_will_exist (button tag)
+  # ========================================================================= #
+  def create_the_button_to_calculate_how_many_bacteria_will_exist
+    # ======================================================================= #
+    # === @button_to_calculate_how_many_bacteria_will_exist
+    # ======================================================================= #
+    @button_to_calculate_how_many_bacteria_will_exist = bold_button(
+      'Calculate how many bacteria will exist after n rounds'
+    )
+    @button_to_calculate_how_many_bacteria_will_exist.clear_background
+    @button_to_calculate_how_many_bacteria_will_exist.bblack2
+    @button_to_calculate_how_many_bacteria_will_exist.on_clicked {
+      do_the_calculation
+    }
+    @button_to_calculate_how_many_bacteria_will_exist.hint =
+      "Click on this button in order to do the calculation\n"\
+      "e. g. <b>how many bacteria we will have</b> "\
+      "based on the above parameters."
+    @button_to_calculate_how_many_bacteria_will_exist.on_hover(:powderblue)
+    # @button_to_calculate_how_many_bacteria_will_exist.bg_colour(
+    #   :lightsteelblue
+    # )
+  end
+
+  # ========================================================================= #
+  # === create_the_entries
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # === @entry_point_start_with_n_bacteria
+    # ======================================================================= #
+    @entry_point_start_with_n_bacteria = entry
+    @entry_point_start_with_n_bacteria.default = 10
+    @entry_point_start_with_n_bacteria.bblack1
+    @entry_point_start_with_n_bacteria.on_click_select_all
+    @entry_point_start_with_n_bacteria.do_center
+    @entry_point_start_with_n_bacteria.on_key_press_event { |widget, event|
+      if use_gtk3?
+        do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
+      else
+        do_the_calculation
+      end
+    }
+    @entry_point_start_with_n_bacteria.hint =
+      'Input a <b>number</b> here, denoting how many bacteria '\
+      'exist at the start.'
+
+    # ======================================================================= #
+    # === @entry_point_use_n_divisions
+    # ======================================================================= #
+    @entry_point_use_n_divisions = entry
+    @entry_point_use_n_divisions.default = 10
+    @entry_point_use_n_divisions.bblack1
+    @entry_point_use_n_divisions.on_click_select_all
+    @entry_point_use_n_divisions.do_center
+    @entry_point_use_n_divisions.on_key_press_event { |widget, event|
+      if use_gtk3?
+        do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
+      else
+        do_the_calculation
+      end
+    }
+    @entry_point_use_n_divisions.hint =
+      'Input a <b>number</b> here, denoting how many cell '\
+      'divisions the bacteria will undergo.'
+
+    # ======================================================================= #
+    # === @entry_point_n_cells
+    # ======================================================================= #
+    @entry_point_n_cells = entry
+    @entry_point_n_cells.default = 0
+    @entry_point_n_cells.bblack1
+    @entry_point_n_cells.do_center
+    @entry_point_n_cells.on_key_press_event { |widget, event|
+      if use_gtk3?
+        do_the_calculation if Gdk::Keyval.to_name(event.keyval) == 'Return'
+      else
+        do_the_calculation
+      end
+    }
+    @entry_point_n_cells.hint =
+      'The number here will be <b>the amount of bacteria '\
+      'after n cell divisions</b>.'
+  end
+
+  # ========================================================================= #
+  # === create_the_boxes
+  # ========================================================================= #
+  def create_the_boxes
+    # ======================================================================= #
+    # === @hbox1
+    # ======================================================================= #
+    @hbox1 = create_hbox(
+      bold_text('n bacteria (start)'),
+      @entry_point_start_with_n_bacteria
+    )
+
+    # ======================================================================= #
+    # === @hbox2
+    # ======================================================================= #
+    @hbox2 = create_hbox(
+      bold_text('n doubling times'),
+      @entry_point_use_n_divisions
+    )
+
+    # ======================================================================= #
+    # === @hbox3
+    # ======================================================================= #
+    @hbox3 = create_hbox(
+      bold_text('n bacteria (end)'),
+      @entry_point_n_cells
+    )
+  end
+
+  # ========================================================================= #
+  # === create_the_hspacer
+  # ========================================================================= #
+  def create_the_hspacer
+    @a_hspacer = hspacer
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_entries
+    create_the_button_to_calculate_how_many_bacteria_will_exist
+    create_the_boxes # Must come after the entries.
+    create_the_hspacer
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+  end
+
+end; end; end