bioroebe 0.10.80

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

@@ -0,0 +1,370 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::HammingDistance
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/hamming_distance/hamming_distance.rb'
+# Bioroebe::GUI::Gtk::HammingDistance.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+require 'bioroebe/constants/GUIs.rb'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class HammingDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::HammingDistance 
+
+  require 'bioroebe/string_matching/hamming_distance.rb'
+  require 'bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb'
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = 500
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 320
+
+  # ========================================================================= #
+  # === TITLE
+  #
+  # Specify which title to use for this small widget.
+  # ========================================================================= #
+  TITLE = 'Hamming Distance'
+    USE_THIS_TITLE = TITLE # === USE_THIS_TITLE
+
+  # ========================================================================= #
+  # === PADDING_TO_USE
+  # ========================================================================= #
+  PADDING_TO_USE = 5
+
+  # ========================================================================= #
+  # === MONOSPACED_FONT
+  #
+  # When this font is changed, don't forget to also change the font
+  # at SMALLER_FONT.
+  # ========================================================================= #
+  MONOSPACED_FONT = :hack_20
+    USE_THIS_FONT = MONOSPACED_FONT
+
+  # ========================================================================= #
+  # === SMALLER_FONT
+  # ========================================================================= #
+  SMALLER_FONT = :hack_16
+
+  # ========================================================================= #
+  # === DEFAULT_TEXT_FOR_ENTRY1
+  # ========================================================================= #
+  DEFAULT_TEXT_FOR_ENTRY1 = 'AGUUCGAUGGAAAATAT'
+
+  # ========================================================================= #
+  # === DEFAULT_TEXT_FOR_ENTRY2
+  # ========================================================================= #
+  DEFAULT_TEXT_FOR_ENTRY2 = 'AGUCCGGUCGAAAAAAA'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      optional_commandline_arguments = nil,
+      run_already                    = true
+    )
+    super(:horizontal)
+    register_sigint
+    reset
+    set_title(USE_THIS_TITLE) if respond_to?(:set_title)
+    if optional_commandline_arguments and respond_to?(:menu)
+      menu(optional_commandline_arguments)
+    end
+    signal_destroy_then_quit
+    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)
+    use_gtk_paradise_project_CSS_file
+    append_project_CSS_file
+    set_border_width(5) 
+    infer_the_size_automatically
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    PADDING_TO_USE
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    0
+  end
+
+  # ========================================================================= #
+  # === seq1?
+  # ========================================================================= #
+  def seq1?
+    @entry_on_top.text
+  end
+
+  # ========================================================================= #
+  # === seq2?
+  # ========================================================================= #
+  def seq2?
+    @entry_on_bottom.text
+  end
+
+  # ========================================================================= #
+  # === set_minimum_size
+  # ========================================================================= #
+  def set_minimum_size
+    set_size_request(80, 100)
+  end
+
+  # ========================================================================= #
+  # === entry1?
+  # ========================================================================= #
+  def entry1?
+    @entry_on_top
+  end
+
+  # ========================================================================= #
+  # === compare_the_two_sequences
+  #
+  # This is the method that will compare the two sequences.
+  # ========================================================================= #
+  def compare_the_two_sequences
+    hamming_distance_object = ::Bioroebe::HammingDistance.new("#{seq1?} #{seq2?}") { :be_quiet }
+    @entry_n_differences.set_text(
+      hamming_distance_object.n_differences?.to_s
+    )
+  end; alias do_compare                   compare_the_two_sequences # === do_compare
+       alias do_calculate_the_differences compare_the_two_sequences # === do_calculate_the_differences
+
+  # ========================================================================= #
+  # === consider_sanitizing_the_input
+  # ========================================================================= #
+  def consider_sanitizing_the_input
+    # ======================================================================= #
+    # The following two lines were added as of 07.05.2020.
+    # ======================================================================= #
+    @entry_on_top.set_text(@entry_on_top.text.delete('-'))
+    @entry_on_bottom.set_text(@entry_on_bottom.text.delete('-'))
+  end
+
+  # ========================================================================= #
+  # === create_entries                               (entries tag, entry tag)
+  # ========================================================================= #
+  def create_entries
+    # ======================================================================= #
+    # === @entry_n_differences
+    #
+    # This is the entry that will simply show the number of differences
+    # between the two sequences, as a number.
+    # ======================================================================= #
+    @entry_n_differences = gtk_entry_with_icon_name('edit-undo-symbolic-rtl.symbolic')
+    @entry_n_differences.xalign = 0.5 # Align towards the center.
+    @entry_n_differences.bblack1
+    @entry_n_differences.clear_background
+    @entry_n_differences.yellow_background
+
+    # ======================================================================= #
+    # === @entry_on_top
+    # ======================================================================= #
+    @entry_on_top = gtk_entry(DEFAULT_TEXT_FOR_ENTRY1)
+    @entry_on_top.set_font(MONOSPACED_FONT)
+    @entry_on_top.clear_background
+    @entry_on_top.css_class('BG_lightsteelblue')
+    @entry_on_top.bblack1
+    @entry_on_top.on_changed { do_calculate_the_differences }
+    @entry_on_top.hint = 'This entry should contain the first sequence (seq1).'
+    @entry_on_top.set_max_length(50_000)
+    @entry_on_top.on_key_press_event { |widget, event|
+      old_text = widget.text
+      keyname = Gdk::Keyval.to_name(event.keyval)
+      case keyname.upcase
+      when *%w( A T C G U )
+        # This is ok.
+      when *%w( B D E F H I J K L M N O P Q R S V W X Y Z ) # Otherwise set the old input here.
+        unless event.state.control_mask? # This snippet checks whether a key-combination has been used.
+          widget.set_text(old_text)
+        end
+      end
+    }
+    # ======================================================================= #
+    # And keep things upcased here:
+    # ======================================================================= #
+    @entry_on_top.on_key_release { |widget, event|
+      old_text = @entry_on_top.text
+      new_text = @entry_on_top.text.upcase
+      unless old_text == new_text
+        @entry_on_top.set_text(new_text)
+        @entry_on_top.move_cursor_to_the_most_right_position
+      end
+    }
+
+    # ======================================================================= #
+    # === @entry_on_bottom
+    # ======================================================================= #
+    @entry_on_bottom = gtk_entry(DEFAULT_TEXT_FOR_ENTRY2)
+    @entry_on_bottom.set_font(MONOSPACED_FONT)
+    @entry_on_bottom.css_classes('clear_background BG_lightsteelblue')
+    @entry_on_bottom.bblack1
+    @entry_on_bottom.on_changed { do_calculate_the_differences }
+    @entry_on_bottom.hint = 'This entry should contain the second sequence (seq2).'
+    @entry_on_bottom.set_max_length(50_000)
+  end
+
+  # ========================================================================= #
+  # === create_compare_button
+  #
+  # This method will create the button that will compare the two sequences.
+  # ========================================================================= #
+  def create_compare_button
+    # ======================================================================= #
+    # === @compare_button
+    # ======================================================================= #
+    @compare_button = bold_button(::Bioroebe::GUI::LevenstheinDistanceModule::TEXT_COMPARE_THE_TWO_SEQUENCES)
+    @compare_button.apply_markup
+    @compare_button.lightblue
+    @compare_button.set_name('button1')
+    @compare_button.hint = 'Click this button to '\
+      '<span weight="bold" foreground="lightblue">compare</span> '\
+      'the two sequences.'
+    @compare_button.on_clicked {
+      consider_sanitizing_the_input
+      compare_the_two_sequences
+    }
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                            (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_entries
+    # ======================================================================= #
+    # === The top box
+    # ======================================================================= #
+    @top_box = gtk_vbox
+
+    @label_on_top = bold_label(USE_THIS_TITLE)
+    @label_on_top.fancy_tooltips = 
+      "Only <b>valid nucleotides</b> (A, T, C, G, U) \n"\
+      "can be accepted as input."
+    # ======================================================================= #
+    # Create the top hbox for string1 next:
+    # ======================================================================= #
+    @hbox_for_string1 = gtk_hbox
+    @hbox_for_string1.minimal(gtk_label('1').make_bold, 1)
+    @hbox_for_string1.maximal(@entry_on_top, 1)
+
+    # ======================================================================= #
+    # Create the bottom hbox for string2 next:
+    # ======================================================================= #
+    @hbox_for_string2 = gtk_hbox
+    @hbox_for_string2.minimal(gtk_label('2').make_bold, 1)
+    @hbox_for_string2.maximal(@entry_on_bottom, 1)
+
+    create_compare_button
+
+    small_hbox = gtk_hbox
+    # ======================================================================= #
+    # === n_differences found Gtk::Text
+    # ======================================================================= #
+    short_text_widget = gtk_text('<b>n differences</b> found:')
+    short_text_widget.do_markify
+    small_hbox.minimal(short_text_widget, 2)
+    small_hbox.hint =
+      'This entry will show <b>how many differences</b> '\
+      'exist between these two strings.'
+    small_hbox.minimal(@entry_n_differences, 2)
+    # ======================================================================= #
+    # === The bottom box
+    # ======================================================================= #
+    @bottom_box = gtk_vbox
+    @bottom_box.pack_start(@compare_button, expand: false, fill: false, padding: 1)
+    @bottom_box.pack_start(small_hbox, expand: false, fill: true, padding: 0)
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    # ======================================================================= #
+    # @top_box is an instance of gtk-vbox.
+    # ======================================================================= #
+    @top_box.minimal(@label_on_top,     1)
+    text = left_aligned_text(
+        "The <b>Hamming distance</b> - a number - measures the number of "\
+        "\npositions at which two strings of equal length are "\
+        "different.")
+    text.use_this_font = SMALLER_FONT
+    @top_box.minimal(text,              12)
+    @top_box.minimal(@hbox_for_string1,  2)
+    @top_box.minimal(@hbox_for_string2,  2)
+
+    vpaned = mouse_draggable_via_up_and_down_movement(@top_box, @bottom_box)
+    vpaned.set_size_request(@width, 550)
+    maximal(vpaned, 8)
+    show_all
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+    set_minimum_size
+    Thread.new {
+      sleep 0.01
+      @entry_n_differences.do_focus
+      entry1?.deselect
+      do_compare
+    }
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::HammingDistance.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::HammingDistance.new(i)
+    r = ::Gtk.run
+    r << _
+    r.modify_background(:normal, :mintcream)
+    r.automatic_size_then_automatic_title
+    r.top_left_then_run
+  end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::HammingDistance.run_gtk3_widget
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::HammingDistance.run
+end # gtkhammingdistance

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

@@ -0,0 +1,6 @@
+width:                                       920
+height:                                      640
+padding:                                       4
+title:                      Levensthein Distance
+favicon:                                 :tabble
+font_in_use:                             Sans 20

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

@@ -0,0 +1,175 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::Gtk::LevenstheinDistance
+#
+# This is just a small widget that bundles together a GUI component
+# towards the Levensthein class.
+# =========================================================================== #
+# require 'bioroebe/gui/gtk3/levensthein_distance/levensthein_distance.rb'
+# Bioroebe::GUI::Gtk::LevenstheinDistance.run
+# =========================================================================== #
+require 'gtk_paradise/require_gtk3'
+
+module Bioroebe
+
+module GUI
+
+module Gtk
+
+class LevenstheinDistance < ::Gtk::Box # === Bioroebe::GUI::Gtk::LevenstheinDistance
+
+  require 'bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb'
+  include Bioroebe::GUI::LevenstheinDistanceModule
+
+  require 'gtk_paradise/requires/require_the_base_module.rb'
+  include ::Gtk::BaseModule
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true
+    )
+    super(:vertical)
+    register_sigint
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    modify_background(
+      :normal, USE_THIS_AS_BACKGROUND_COLOUR_FOR_THE_WIDGET
+    )
+    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)
+    use_gtk_paradise_project_CSS_file
+    append_project_CSS_file 
+    infer_the_size_automatically
+    instantiate_a_new_levensthein_object
+  end
+
+  # ========================================================================= #
+  # === create_the_grid                                            (grid tag)
+  # ========================================================================= #
+  def create_the_grid
+    # ======================================================================= #
+    # === @grid
+    # ======================================================================= #
+    @grid = gtk_grid
+    @grid.set_column_spacing(4)
+    @grid.set_row_spacing(4)
+  end
+
+  # ========================================================================= #
+  # === populate_the_grid
+  # ========================================================================= #
+  def populate_the_grid
+    @grid.left(@text1)
+    @grid.right(@input_field_for_matches)
+    @grid.new_row
+    @grid.left(@text2)
+    @grid.right(@input_field_for_mismatches)
+    @grid.new_row
+    @grid.left(@text3)
+    @grid.right(@input_field_for_gap_cost)
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    populate_the_grid
+    minimal(@grid, 4)
+    if levensthein_object?.sequence1?
+      unless levensthein_object?.sequence1?.empty?
+        @input_for_string1.set_text(levensthein_object?.sequence1?)
+      end
+    end
+    if levensthein_object?.sequence2?
+      unless levensthein_object?.sequence2?.empty?
+        @input_for_string2.set_text(levensthein_object?.sequence2?)
+      end
+    end
+    minimal(@input_for_string1, 4)
+    minimal(@input_for_string2, 4)
+    # ======================================================================= #
+    # 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
+    )
+    minimal(@hbox_with_the_label_for_the_edit_distance, 4)
+    minimal(@hbox4, 4)
+    button_box = gtk_button_box(
+      @button_compare_the_two_strings
+    ) { :spread }
+    minimal(button_box, 4)
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_entries
+    create_the_labels
+    create_the_grid
+    create_the_first_row
+    create_the_second_row
+    create_the_third_row
+    create_the_buttons
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+    show_all
+    check_for_commandline_arguments
+    do_compare_the_two_sequences
+    let_the_fist_entry_respond_to_on_changed_events
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::LevenstheinDistance.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::LevenstheinDistance.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic_size_then_automatic_title
+    r.top_left_then_run
+  end; self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::LevenstheinDistanceModule.start_gui_application
+       self.instance_eval { alias run_gtk3_widget       run } # === Bioroebe::GUI::Gtk::LevenstheinDistance.run_gtk3_widget
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::Gtk::LevenstheinDistance.run
+end