bioroebe 0.12.24 → 0.13.31

data/lib/bioroebe/gui/universal_widgets/alignment/alignment.rb

@@ -0,0 +1,557 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::UniversalWidgets::Alignment
+#
+#
+# Usage example:
+#
+#   Bioroebe::GUI::UniversalWidgets::Alignment.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/universal_widgets/alignment/alignment.rb'
+# =========================================================================== #
+require 'universal_widgets/base/base.rb'
+
+module Bioroebe
+
+module GUI
+
+module UniversalWidgets
+
+class Alignment < ::UniversalWidgets::Base # === Bioroebe::GUI::UniversalWidgets::Alignment
+
+  require 'bioroebe/base/commandline_application/commandline_arguments.rb'
+  include ::Bioroebe::CommandlineArguments
+
+  require 'bioroebe/constants/GUIs.rb'
+  require 'bioroebe/toplevel_methods/toplevel_methods.rb'
+  require 'bioroebe/sequence/alignment.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Alignment'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '65% or 500px minimum'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '55% or 300px minimum'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :hack_26
+
+  # ========================================================================= #
+  # === FONT_FOR_THE_ENTRIES
+  #
+  # The entries must use a mono-spaced font.
+  # ========================================================================= #
+  FONT_FOR_THE_ENTRIES = :hack_22
+
+  # ========================================================================= #
+  # === TEXT_INPUT_THE_SEQUENCES
+  # ========================================================================= #
+  TEXT_INPUT_THE_SEQUENCES = 'Input the sequences that you wish '\
+                             'to compare to one another'
+
+  # ========================================================================= #
+  # === TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
+  # ========================================================================= #
+  TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON =
+    "Click on this button to analyse the given sequence. Make sure "\
+    "to use <b>newlines</b> in order to split the sequence at hand."
+
+  # ========================================================================= #
+  # === TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE
+  #
+  # This is the base-tooltip for the entry that retains our consensus
+  # sequence.
+  # ========================================================================= #
+  TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE = 
+    'This entry will contain the <b>consensus sequence</b>, '\
+    'derived from the above sequences.'
+
+  # ========================================================================= #
+  # === TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
+  # ========================================================================= #
+  TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION = 
+    "\n\nTake note that in the event that there is <b>an even number of "\
+    "input sequences</b>, the entries defined before will take precedence. "\
+    "So, for instance, if you have four sequences in total, where two are "\
+    "ATTA and the next two are ATTT, then the consensus sequence is "\
+    "currently assumed to be <b>ATTA</b>."
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = nil,
+      run_already           = true
+    )
+    determine_the_GUI_to_be_used(commandline_arguments)
+    reset
+    set_commandline_arguments(
+      commandline_arguments
+    )
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    super() if respond_to?(:super)
+    reset_the_internal_variables
+    reset_the_base_module # This must come after reset_the_internal_variables().
+    infer_the_namespace
+    # ======================================================================= #
+    # === @configuration
+    # ======================================================================= #
+    @configuration = [true, __dir__, namespace?]
+    # ======================================================================= #
+    # === Set the title, width, height and the font in use.
+    # ======================================================================= #
+    title_width_height_font(TITLE, WIDTH, HEIGHT, USE_THIS_FONT)
+    handle_CSS if use_gtk3?
+    reset_the_alignment_object
+  end
+
+  # ========================================================================= #
+  # === handle_CSS_rules                                            (CSS tag)
+  # ========================================================================= #
+  def handle_CSS_rules
+    use_gtk_paradise_project_css_file
+    append_project_css_file
+    apply_the_CSS_rules
+  end; alias handle_CSS handle_CSS_rules # === handle_CSS
+
+  # ========================================================================= #
+  # === return_the_first_row
+  # ========================================================================= #
+  def return_the_first_row
+    _ = create_hbox
+    top_label = left_aligned_label(
+      TEXT_INPUT_THE_SEQUENCES
+    )
+    top_label.make_selectable
+    top_label.center
+    _.minimal(top_label)
+    use_this_image = image_document_open
+    if use_this_image
+      event_box = event_box(use_this_image)
+      if event_box
+        event_box.hint = 'Click on this icon to open a local file.'
+        event_box.on_clicked {
+          do_open_and_assign_a_local_file
+        }
+        _.pack_end(event_box)
+      end
+    end
+    return _
+  end
+
+  # ========================================================================= #
+  # === create_the_entries                           (entry tag, entries tag)
+  # ========================================================================= #
+  def create_the_entries
+    create_the_consensus_sequence_entry
+    # ======================================================================= #
+    # === @entry_numbers
+    # ======================================================================= #
+    @entry_numbers = create_entry
+    @entry_numbers.bblack1
+    @entry_numbers.use_this_font = FONT_FOR_THE_ENTRIES
+    @entry_numbers.hint =
+      'This area may indicate the numbers for '\
+      'the alignment shown right above.'
+    @entry_numbers.very_light_yellow_background
+  end
+
+  # ========================================================================= #
+  # === create_the_text_buffer_and_the_text_view
+  # ========================================================================= #
+  def create_the_text_buffer_and_the_text_view
+    # ======================================================================= #
+    # === @text_buffer
+    # ======================================================================= #
+    @text_buffer = create_text_buffer
+    # ======================================================================= #
+    # === @text_view
+    # ======================================================================= #
+    @text_view = create_text_view(@text_buffer)
+  end
+
+  # ========================================================================= #
+  # === textview?
+  # ========================================================================= #
+  def textview?
+    @text_view
+  end
+
+  # ========================================================================= #
+  # === create_the_scrolled_window
+  # ========================================================================= #
+  def create_the_scrolled_window
+    # ======================================================================= #
+    # === @scrolled_window
+    # ======================================================================= #
+    @scrolled_window = create_scrolled_window(@text_view)
+    @scrolled_window.width_height(300, 400)
+    @scrolled_window.pad4px
+    @scrolled_window.bblack2
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    12
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    8
+  end
+
+  # ========================================================================= #
+  # === smaller_font?
+  # ========================================================================= #
+  def smaller_font?
+    SMALLER_FONT
+  end
+
+  # ========================================================================= #
+  # === the_do_analyse_button_was_clicked
+  # ========================================================================= #
+  def the_do_analyse_button_was_clicked
+    do_analyse
+    realign_the_numbers_showing_how_long_the_consensus_sequence_is
+    update_the_hint_for_the_entry_consequences_sequence(
+      (
+        "This entry will contain the consensus sequence, "\
+        "derived from the above "+
+        (@text_buffer.text?.count("\n")+1).to_s+" sequences.\n\nNote "\
+        "that only the minimal length will be compared - "\
+        "superfluous nucleotides will NOT be considered unless "\
+        "they can be aligned to other sequences."+
+        TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
+      ).squeeze(' ')
+    )
+  end
+
+  # ========================================================================= #
+  # === create_the_skeleton                        (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_the_skeleton
+    create_the_checkboxes # Create the checkboxes first.
+    create_the_entries
+    create_the_buttons
+    create_the_text_buffer_and_the_text_view
+    create_the_scrolled_window
+  end
+
+  # ========================================================================= #
+  # === create_the_checkboxes
+  # ========================================================================= #
+  def create_the_checkboxes
+    # ======================================================================= #
+    # === @checkbox1
+    # ======================================================================= #
+    @checkbox1 = create_checkbox
+    @checkbox1.is_active
+    @checkbox2 = create_checkbox
+  end
+
+  # ========================================================================= #
+  # === button_convert?
+  # ========================================================================= #
+  def button_convert?
+    @button_convert
+  end
+
+
+  # ========================================================================= #
+  # === create_the_buttons                                      (buttons tag)
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @button_do_analyse
+    # ======================================================================= #
+    @button_do_analyse = bold_button('_Do analyse', self, :use_mnemonic) {
+      :the_do_analyse_button_was_clicked
+    }
+    @button_do_analyse.clear_background
+    @button_do_analyse.bblack1
+    @button_do_analyse.on_hover(:lightblue)
+    @button_do_analyse.hint = TOOLTIP_HINT_FOR_THE_DO_ANALYSE_BUTTON
+  end
+
+  # ========================================================================= #
+  # === do_trigger_the_conversion                            (conversion tag)
+  #
+  # This method is the one that will convert from the three-letter to the
+  # one-letter and vice versa.
+  # ========================================================================= #
+  def do_trigger_the_conversion(
+      i         = @entry1.text?,
+      checkbox1 = @checkbox1
+    )
+    i = i.to_s.dup.delete(' ')
+    if checkbox1.active?
+      new_result = Bioroebe.three_to_one(i).to_s
+    else
+      new_result = Bioroebe.one_to_three(i).to_s
+    end
+    if new_result and !new_result.empty?
+      @entry2.set_text(new_result)
+      @entry2.make_bold
+    end
+  end; alias do_the_conversion do_trigger_the_conversion # === do_the_conversion
+
+  # ========================================================================= #
+  # === return_the_checkbox_widget
+  # ========================================================================= #
+  def return_the_checkbox_widget
+    smaller_font = smaller_font?
+    grid = default_grid
+    text1 = text('3-to-1 conversion')
+    text1.use_this_font(smaller_font)
+    text1.hint = 'Convert the three letter code to the one letter code.'
+pp text1
+    grid.left(text1)
+    grid.right(@checkbox1)
+    text2 = text('1-to-3 conversion')
+    text2.use_this_font(smaller_font)
+    text2.hint = 'Convert the one letter code to the three letter code.'
+    grid.left(text2)
+    grid.right(@checkbox2)
+    @checkbox1.on_toggled {
+      if @checkbox1.active? == false
+        @checkbox2.is_now_active
+      else
+        @checkbox2.is_now_inactive
+      end
+    }
+    @checkbox2.on_toggled {
+      if @checkbox2.active? == false
+        @checkbox1.is_now_active
+      else
+        @checkbox1.is_now_inactive
+      end
+    }
+    return grid
+  end
+
+  # ========================================================================= #
+  # === do_analyse
+  #
+  # This method will be called whenever the user hits the "Do analyse"
+  # button.
+  # ========================================================================= #
+  def do_analyse(
+      _ = text_buffer?.text?
+    )
+    if _ and !_.empty?
+      _.strip!
+      alignment?.use_this_as_input(_)
+      consensus_sequence = return_the_consensus_sequence
+      @entry_consensus_sequence.set_text(consensus_sequence)
+    else
+      pop_up_widget(
+        over_this_widget: text_view_widget?,
+        text:             'Please assign a sequence first.'
+      )
+    end
+  end; alias do_analyse_again do_analyse # === do_analyse_again
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    run_super
+  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
+
+  # ========================================================================= #
+  # === create_the_consensus_sequence_entry
+  # ========================================================================= #
+  def create_the_consensus_sequence_entry
+    # ======================================================================= #
+    # === @entry_consensus_sequence
+    # ======================================================================= #
+    @entry_consensus_sequence = entry
+    @entry_consensus_sequence.bblack1
+    @entry_consensus_sequence.center
+    @entry_consensus_sequence.use_this_font = FONT_FOR_THE_ENTRIES
+    @entry_consensus_sequence.yellow_background
+    update_the_hint_for_the_entry_consequences_sequence(
+      TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE+
+      TOOLTIP_HINT_FOR_THE_ENTRY_CONSENSUS_SEQUENCE_TRAILING_INFORMATION
+    )
+  end
+
+  # ========================================================================= #
+  # === entry_consensus_sequence?
+  # ========================================================================= #
+  def entry_consensus_sequence?
+    @entry_consensus_sequence
+  end
+
+  # ========================================================================= #
+  # === return_fill_up_to
+  # ========================================================================= #
+  def return_fill_up_to(i)
+    _ = ''.dup
+    i.times {|counter|
+      counter = (counter+1) % 10
+      _ << counter.to_s
+    }
+    return _
+  end
+
+  # ========================================================================= #
+  # === do_open_and_assign_a_local_file
+  # ========================================================================= #
+  def do_open_and_assign_a_local_file
+    open_local_file {{
+      start_directory: log_dir?,
+      additional_folders: [
+        log_dir?,
+        '/Depot/j/',
+        '/Depot/jj/',
+        '/Depot/jjj/',
+        '/Depot/jjjj/'
+      ]
+    }}
+    _ = main_file?
+    if _ and File.exist?(_)
+      dataset = File.read(_)
+      @text_buffer.set_text(dataset)
+      do_analyse_again
+    end
+  end
+
+  # ========================================================================= #
+  # === update_the_hint_for_the_entry_consequences_sequence
+  # ========================================================================= #
+  def update_the_hint_for_the_entry_consequences_sequence(
+      i = ''
+    )
+    @entry_consensus_sequence.hint = i
+  end
+
+  # ========================================================================= #
+  # === alignment?
+  # ========================================================================= #
+  def alignment?
+    @alignment
+  end
+
+  # ========================================================================= #
+  # === text_buffer?
+  # ========================================================================= #
+  def text_buffer?
+    @text_buffer
+  end
+
+  # ========================================================================= #
+  # === reset_the_alignment_object
+  # ========================================================================= #
+  def reset_the_alignment_object
+    # ======================================================================= #
+    # === @alignment
+    # ======================================================================= #
+    @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::UniversalWidgets::Alignment[]
+  # ========================================================================= #
+  def self.[](i = ARGV)
+    new(i)
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::Alignment.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    ::Gtk.gtk_runner_factory(
+      ::Bioroebe::GUI::Gtk::Alignment.new(i)
+    )
+  end
+
+  # ========================================================================= #
+  # === connect_the_skeleton                      (connect tag, skeleton tag)
+  # ========================================================================= #
+  def connect_the_skeleton
+    abort_on_exception
+    
+    grid = default_grid
+    grid.full_row(return_the_first_row)
+    grid.full_row(@scrolled_window)
+    grid.full_row(@entry_consensus_sequence)
+    grid.full_row(@entry_numbers)
+    grid.full_row(@button_do_analyse)
+    grid.hcenter
+
+    window = runner_widget(nil, width?, height?, title?)
+    window << grid
+    do_focus_on_the_textview
+    ::UniversalWidgets.set_main_window(window)
+    upon_delete_event_quit_the_application
+    window.use_this_font = font?
+    window.show_all
+    window.set_size_request(width?, height?)
+    window.set_default_size(width?, height?)
+    window.set_padding(padding?)
+    window.set_border_size(border_size?)
+    window.top_left
+    run_main
+  end
+
+  # ========================================================================= #
+  # === do_focus_on_the_textview
+  # ========================================================================= #
+  def do_focus_on_the_textview
+    textview?.do_focus
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::UniversalWidgets::Alignment.new(ARGV)
+end # gui_alignment