bioroebe 0.10.80

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

@@ -0,0 +1,135 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::LibUI::HammingDistance
+# =========================================================================== #
+require 'bioroebe/constants/GUIs.rb'
+
+module Bioroebe
+
+module GUI
+
+module LibUI
+
+module HammingDistance # === Bioroebe::GUI::LibUI::HammingDistance
+
+  require 'libui_paradise/autoinclude'
+  include LibuiParadise::Extensions
+
+  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+  require 'bioroebe/toplevel_methods/misc.rb'
+  require 'bioroebe/codons/codons.rb'
+  require 'bioroebe/string_matching/hamming_distance.rb'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    # ======================================================================= #
+    # === @entry_n_differences
+    # ======================================================================= #
+    @entry_n_differences = UI.entry
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    create_skeleton
+    main_window = ui_margined_window('Hamming Distance', 1200, 200, 0)
+    # ======================================================================= #
+    # Next add the two hboxes that will contain the two sequences.
+    # ======================================================================= #
+    text_changed_callback = proc { |ptr|
+      text = text?(ptr)
+      upcased_text = text.upcase
+      UI.entry_set_text(ptr, upcased_text)
+    }
+
+    hbox1  = ui_padded_hbox
+    text1  = text(1)
+    @entry1 = ui_entry('ATG')
+    UI.entry_on_changed(@entry1, text_changed_callback, nil)
+    hbox1.add(text1, 1)
+    hbox1.add(@entry1, 1)
+    hbox1.set_padded(1)
+
+    hbox2  = ui_padded_hbox
+    text2  = text(2)
+    @entry2 = ui_entry('ATT')
+    UI.entry_on_changed(@entry2, text_changed_callback, nil)
+    hbox2.add(text2, 1)
+    hbox2.add(@entry2, 1)
+    hbox2.set_padded(1)
+
+    hbox_compare_the_two_sequences = ui_hbox
+    # ======================================================================= #
+    # The hbox that has the "n differences found".
+    # ======================================================================= #
+    hbox_n_differences_found = ui_hbox
+    button_compare_the_two_sequences = ui_button('Compare the two sequences')
+    button_compare_the_two_sequences.on_clicked {
+      text1 = UI.entry_text(@entry1)
+      text2 = UI.entry_text(@entry2)
+      compare_the_two_sequences(text1, text2, @entry_n_differences)
+      0
+    }
+    hbox_compare_the_two_sequences.add(button_compare_the_two_sequences, 1)
+    hbox_n_differences_found.add(text('n differences found'), 1)
+    hbox_n_differences_found.add(@entry_n_differences, 1)
+    # ======================================================================= #
+    # This is the main vbox.
+    # ======================================================================= #
+    vbox = ui_padded_vbox
+    vbox.maximal(text('Hamming Distance'))
+    vbox.maximal(
+      text(
+        "The Hamming distance - a number - measures the number of "\
+        "\npositions at which two strings of equal length are "\
+        "different."
+      )
+    )
+    vbox.maximal(hbox1)
+    vbox.add(hbox2, 1)
+    vbox.add(hbox_compare_the_two_sequences, 1)
+    vbox.add(hbox_n_differences_found, 1)
+    main_window.child = vbox
+    main_window.control_show
+    main_window.elegant_exit
+  end
+
+  # ========================================================================= #
+  # === compare_the_two_sequences
+  #
+  # This is the method that will compare the two sequences.
+  # ========================================================================= #
+  def compare_the_two_sequences(
+      seq1, seq2, entry
+    )
+    hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1} #{seq2}") { :be_quiet }
+    _ = hamming_distance_object.n_differences?.to_s
+    UI.entry_set_text(entry, _)
+  end; alias do_compare                   compare_the_two_sequences # === do_compare
+       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::LibUI::HammingDistance.run
+  # ========================================================================= #
+  def self.run
+    object = Object.new
+    object.extend(HammingDistance)
+    object.run
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::LibUI::HammingDistance.run
+end

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

@@ -0,0 +1,118 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::LibUI::LevenstheinDistance
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module LibUI
+
+class LevenstheinDistance # === Bioroebe::GUI::LibUI::LevenstheinDistance
+
+  require 'libui_paradise'
+  include LibuiParadise::Extensions
+
+  require 'bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb'
+  include Bioroebe::GUI::LevenstheinDistanceModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    set_title(TITLE)
+    set_width(WIDTH)
+    set_height(HEIGHT)
+    instantiate_a_new_levensthein_object
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                            (skeleton tag, create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_entries
+    create_the_labels
+    create_the_first_row
+    create_the_second_row
+    create_the_third_row
+    create_the_buttons
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    create_skeleton
+    window = ui_padded_main_window(title?, width?, height?, 0)
+    outer_vbox = padded_vbox
+
+    hbox1 = hbox(@text1, @input_field_for_matches)
+    outer_vbox.minimal(hbox1)
+    outer_vbox.add_hsep
+
+    hbox2 = hbox(@text2, @input_field_for_mismatches)
+    outer_vbox.minimal(hbox2)
+    outer_vbox.add_hsep
+
+    hbox3 = hbox(@text3, @input_field_for_gap_cost)
+    outer_vbox.minimal(hbox3)
+    outer_vbox.add_hsep
+
+    outer_vbox.minimal(@input_for_string1)
+    outer_vbox.minimal(@input_for_string2)
+    outer_vbox.add_hsep
+    # ======================================================================= #
+    # Next below these two input-fields we will add more info:
+    # ======================================================================= #
+    small_label = return_the_edit_distance_label
+    @hbox_with_the_label_for_the_edit_distance = return_hbox_containing_the_edit_distance(
+      small_label, @label_for_the_edit_distance
+    )
+    @hbox4 = return_hbox4(
+      @label_for_the_total_score
+    )
+    outer_vbox.minimal(@hbox_with_the_label_for_the_edit_distance, 4)
+    outer_vbox.minimal(@hbox4, 4)
+
+    button = @button_compare_the_two_strings
+    outer_vbox.minimal(button, 0)
+
+    hbox_on_bottom = padded_hbox
+    button_quit = quit_button
+    hbox_on_bottom.maximal(button_quit)
+    outer_vbox.minimal(hbox_on_bottom)
+
+    check_for_commandline_arguments
+    do_compare_the_two_sequences
+    let_the_fist_entry_respond_to_on_changed_events
+
+    window.add(outer_vbox)
+    window.intelligent_exit
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::LibUI::LevenstheinDistance.new  
+end

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

@@ -0,0 +1,115 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::LibUI::ProteinToDNA
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module LibUI
+
+class ProteinToDNA # === Bioroebe::GUI::LibUI::ProteinToDNA
+
+  require 'libui_paradise'
+  include LibuiParadise::Extensions
+
+  alias e puts
+
+  require 'bioroebe/constants/GUIs.rb'
+  include ::Bioroebe::GUI
+
+  require 'bioroebe/conversions/convert_aminoacid_to_dna.rb'
+  require 'bioroebe/toplevel_methods/aminoacids_and_proteins.rb'
+
+  require 'bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb'
+  include Bioroebe::GUI::ProteinToDNAModule
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      run_already = true
+    )
+    reset
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    shared_reset
+  end
+
+  # ========================================================================= #
+  # === create_right_buffer
+  # ========================================================================= #
+  def create_right_buffer
+    @dataset[:right_buffer] = ui_text_view # The right text view.
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                        (skeleton tag)
+  # ========================================================================= #
+  def create_skeleton
+    @outer_vbox = vbox
+    create_buttons
+    create_left_buffer  # Our left buffer.
+    create_right_buffer # Our right buffer.
+    create_top_hbox
+  end
+
+  # ========================================================================= #
+  # === create_top_hbox
+  # ========================================================================= #
+  def create_top_hbox
+    top_hbox = hbox
+    top_hbox.maximal(left?)
+    top_hbox.maximal(right?)
+    @dataset[:top_hbox] = top_hbox
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    @outer_vbox = padded_vbox
+    @outer_vbox.add_hsep
+    @outer_vbox.maximal(@dataset[:top_hbox], 4)
+    button_box = hbox(
+      @dataset[:backtrack_button],
+      @dataset[:quit_button]
+    )
+    @outer_vbox.minimal(button_box)
+    window = ui_padded_main_window(
+      @title,
+      @width,
+      @height,
+      0
+    )
+    window.add(@outer_vbox)
+    window.intelligent_exit
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+  end
+
+  # ========================================================================= #
+  # === create_left_buffer
+  # ========================================================================= #
+  def create_left_buffer
+    @dataset[:left_buffer] = ui_text_view # The left text view.
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::LibUI::ProteinToDNA.new  
+end

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

@@ -0,0 +1,174 @@
+#!/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?
+    )
+    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_s
+    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
+
+  # ========================================================================= #
+  # === 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

@@ -0,0 +1,132 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::LibUI::ShowCodonTable
+# =========================================================================== #
+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