bioroebe 0.10.80

data/lib/bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb

@@ -0,0 +1,519 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::Gui::AntiSenseStrand
+#
+# This widget contains two entries (user input fields). These two entries
+# correspond to sense and anti-sense in a DNA strand.
+#
+# In the first entry the user may only enter "atcg". These will be
+# UPCASED automatically, so the real input will be "ATCG",
+# respectively.
+#
+# Usage example:
+#
+#   Bioroebe::GUI::AntiSenseStrand.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/unified_widgets/anti_sense_strand/anti_sense_strand.rb'
+# Bioroebe::GUI::AntiSenseStrand.new(ARGV)
+# =========================================================================== # 
+module Bioroebe
+
+module GUI
+
+class AntiSenseStrand # === Bioroebe::GUI::AntiSenseStrand
+
+  begin
+    require 'simple_widgets'
+    include SimpleWidgets
+    extend SimpleWidgets
+  rescue LoadError; end
+
+  require 'bioroebe/constants/GUIs.rb'
+  include Bioroebe::GUI
+
+  # ========================================================================= #
+  # Toggle the GUI in use here after setting a default:
+  # ========================================================================= #
+  # use :gtk3
+  use :libui
+
+  # ========================================================================= #
+  # === NAMESPACE
+  # ========================================================================= #
+  NAMESPACE = inspect
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Sense / Anti-Sense Strand'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH  = 840
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 400
+
+  # ========================================================================= #
+  # === MAX_LENGTH
+  # ========================================================================= #
+  MAX_LENGTH = 50_000
+
+  # ========================================================================= #
+  # === IMG_DNA_HELIX
+  # ========================================================================= #
+  IMG_DNA_HELIX =
+    '/home/x/data/images/science/biology/DNA_HELIX.jpg'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = 'Hack 20'
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      commandline_arguments = ARGV,
+      run_already           = true,
+      &block
+    )
+    parse_this_input_for_proper_widget_support(
+      commandline_arguments
+    )
+    register_sigint
+    reset
+    @use_this_as_the_options_hash = {
+      margin: true
+    }
+    # ======================================================================= #
+    # === Handle blocks next
+    # ======================================================================= #
+    if block_given?
+      yielded = yield
+    elsif use_gtk3?
+      yielded = :use_vbox_on_the_toplevel
+    else
+      yielded = nil
+    end
+    case yielded
+    # ===================================================================== #
+    # === :use_vbox_on_the_toplevel
+    # ===================================================================== #
+    when :use_vbox_on_the_toplevel
+      @use_this_as_the_options_hash.update(
+        use_vbox_on_the_toplevel: true
+      )
+    end
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    reset_the_internal_variables
+    # ======================================================================= #
+    # === @configuration
+    # ======================================================================= #
+    @configuration = [true, __dir__, NAMESPACE]
+    title_width_height(TITLE, WIDTH, HEIGHT)
+    use_gtk_paradise_project_css_file
+    append_project_CSS_file
+    # ======================================================================= #
+    # === @callback_quit
+    # ======================================================================= #
+    @callback_quit = Proc.new { quit }
+    # ======================================================================= #
+    # === @callback_new_file
+    # ======================================================================= #
+    @callback_new_file = Proc.new { e 'This is supposed to create a new file.' }
+  end
+
+  # ========================================================================= #
+  # === synchronize_anti_sense
+  #
+  # Will fetch content and synchronize the @entry_anti_sense
+  # ========================================================================= #
+  def synchronize_anti_sense
+    this_text = ''.dup
+    @entry_sense.text?.each_char { |char|
+      case char
+      when 'A' then this_text << 'T'
+      when 'T' then this_text << 'A'
+      when 'C' then this_text << 'G'
+      when 'G' then this_text << 'C'
+      end
+    }
+    @entry_anti_sense.set_text(this_text)
+  end
+
+  # ========================================================================= #
+  # === create_the_entries                                      (entries tag)
+  #
+  # The Sense strand has the uppercased ATGC variant.
+  # ========================================================================= #
+  def create_the_entries
+    # ======================================================================= #
+    # === @entry_sense
+    # ======================================================================= #
+    @entry_sense = entry
+    @entry_sense.yellow_background
+    @entry_sense.bblack1
+    @entry_sense.position = 12
+    @entry_sense.use_this_font = USE_THIS_FONT
+    @entry_sense.on_key_press_event { |w,event|
+      handle_sense(event)
+    }
+    @entry_sense.set_max_length(MAX_LENGTH)
+
+    # ======================================================================= #
+    # === @entry_anti_sense
+    # ======================================================================= #
+    @entry_anti_sense = entry
+    @entry_anti_sense.yellow_background
+    @entry_anti_sense.bblack1
+    @entry_anti_sense.editable = false
+    @entry_anti_sense.use_this_font = USE_THIS_FONT
+    @entry_anti_sense.set_max_length(MAX_LENGTH)
+    # @entry_anti_sense.on_button_press_event { |w, e|
+    #   @entry_anti_sense.do_focus
+    #   # @entry_anti_sense.select_everything
+    # }
+  end
+
+  # ========================================================================= #
+  # === create_the_boxes
+  # ========================================================================= #
+  def create_the_boxes
+    # ======================================================================= #
+    # === @outer_vbox
+    # ======================================================================= #
+    @outer_vbox = padded_vbox
+    @box_with_small_buttons = padded_hbox
+  end
+
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    4
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    2
+  end
+
+  # ========================================================================= #
+  # === create_the_main_window
+  # ========================================================================= #
+  def create_the_main_window
+    @main_window = window(
+      @title,
+      @width,
+      @height,
+      @use_this_as_the_options_hash
+    )
+    @main_window.enable_free_form_css
+    @main_window.try_to_use_this_font(USE_THIS_FONT)
+  end
+
+  # ========================================================================= #
+  # === create_the_buttons                          (buttons tag, button tag)
+  #
+  # This method will create the various buttons for this application.
+  # ========================================================================= #
+  def create_the_buttons
+    # ======================================================================= #
+    # === @button_reset
+    # ======================================================================= #
+    @button_reset = bold_button('_Reset Sense Anti Sense')
+    @button_reset.hint = 'Click on this button to '\
+      '<b>reset</b> again to <b>the initial state '\
+      'of this widget</b>.'
+    @button_reset.clear_background
+    @button_reset.bblack1
+    @button_reset.modify_background(:active,   :lightblue)
+    @button_reset.modify_background(:prelight, :steelblue)
+    @button_reset.modify_background(:normal,   :lightblue)
+    @button_reset.on_clicked {
+      on_reset_action_called
+    }
+    # ======================================================================= #
+    # Next add the four buttons for A, T, C and G.
+    # ======================================================================= #
+    @button_A = coloured_button('A_'+colour_for(:a)) 
+    @button_A.on_clicked { handle_sense('A') }
+    @button_A.popup_hint('Add A (for Adenine) to the sense-strand on top.')
+    @button_A.bblack1
+    @box_with_small_buttons.minimal(@button_A, 2)
+
+    @button_T = coloured_button('T_'+colour_for(:t))
+    @button_T.on_clicked { handle_sense('T') }
+    @button_T.popup_hint('Add T (for Thymine) to the sense-strand on top.')
+    @button_T.bblack1
+    @box_with_small_buttons.minimal(@button_T, 2)
+
+    @button_C = coloured_button('C_'+colour_for(:c))
+    @button_C.on_clicked { handle_sense('C') }
+    @button_C.popup_hint('Add C (for Cytosin) to the sense-strand on top.')
+    @button_C.bblack1
+    @box_with_small_buttons.minimal(@button_C, 2)
+
+    @button_G = coloured_button('G_'+colour_for(:g))
+    @button_G.on_clicked { handle_sense('G') }
+    @button_G.popup_hint('Add G (for Guanine) to the sense-strand on top.')
+    @button_G.bblack1
+    @box_with_small_buttons.minimal(@button_G, 2)
+    do_style_all_the_buttons
+  end
+
+  # ========================================================================= #
+  # === do_style_all_the_buttons
+  # ========================================================================= #
+  def do_style_all_the_buttons(
+      i = return_all_buttons
+    )
+    i.each {|this_button|
+      this_button.set_name('button1')
+      this_button.bblack2
+    }
+  end
+
+  # ========================================================================= #
+  # === colour_for
+  #
+  # Use this method to return a colour for the 4 nucleotides.
+  # ========================================================================= #
+  def colour_for(i)
+    case i
+    when :a
+      'whitesmoke'
+    when :t
+      'teal'
+    when :c
+      'slateblue'
+    when :g
+      'red'
+    end
+  end
+  
+  # ========================================================================= #
+  # === on_reset_action_called
+  # ========================================================================= #
+  def on_reset_action_called
+    # e 'Cleaning up.' # <- If we want to be extra-chatty.
+    @entry_sense.set_text('')
+    @entry_anti_sense.set_text('')
+    @entry_sense.set_focus(true)
+    @entry_sense.position = 12
+  end
+
+  # ========================================================================= #
+  # === focus
+  #
+  # Use this method to focus.
+  # ========================================================================= #
+  def focus(where)
+    case where
+    when ':left'
+      @entry_sense.set_focus(true) 
+    when ':right'
+      @entry_anti_sense.set_focus(true)
+    end
+  end
+
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+  end
+
+  # ========================================================================= #
+  # === create_and_add_menu                                        (menu tag)
+  # ========================================================================= #
+  def create_and_add_menu
+    return # This is currently not in use. Perhaps at a later time.
+    @menu_bar = gtk_menu_bar
+    @menu_item1 = gtk_menu_item('Options')
+    @menu_item1.set_submenu(@first_submenu = gtk_menu)
+    @menu_bar.append(@menu_item1)
+    @menu_actions = [
+      ['FileMenu', nil, '_File'],
+      ['Quit', ::Gtk::Stock::QUIT, '_Quit', 'Q', 'Quit', @callback_quit],
+      ['New',  ::Gtk::Stock::NEW,  '_New',  'N', 'Create a new file', @callback_new_file]
+    ]
+  end
+
+  # ========================================================================= #
+  # === create_the_grid                                            (grid tag)
+  # ========================================================================= #  
+  def create_the_grid
+    # ======================================================================= #
+    # Use a table for the main UI.
+    # ======================================================================= #
+    @grid = default_grid
+    @grid.set_column_spacing(3)
+    @grid.set_row_spacing(3)
+    @grid.pad10px
+  end
+
+  # ========================================================================= #
+  # === populate_the_grid
+  # ========================================================================= #
+  def populate_the_grid
+    label_sense = bold_label('SENSE')
+    @grid.left(label_sense)
+    @grid.right(@entry_sense)
+    label_antisense = bold_label('ANTISENSE')
+    # Next comes a hbox with an image, which is located in the middle.
+    hbox_with_entry_sense_and_image = hbox
+    hbox_with_entry_sense_and_image.add(label_antisense)
+    # The image in the middle.
+    @image = image(IMG_DNA_HELIX)
+    if @image
+      @eventbox = event_box(@image)
+      # ======================================================================= #
+      # === @eventbox
+      #
+      # It is associated with an Eventbox. When we click with a mouse button
+      # on that image in the middle, the following code will be run.
+      # ======================================================================= #
+      @eventbox.signal_connect(:event) { |widget, event|
+        case event.event_type.name.to_s
+        when 'GDK_BUTTON_PRESS'
+          if    event.button == 1 # left   mouse click
+            _ = @entry_sense.text # Feedback the current content.
+            e _
+            if Object.const_defined? :XorgBuffer
+              XorgBuffer[_.chomp]
+            end
+          elsif event.button == 2 # middle mouse click
+          elsif event.button == 3 # right  mouse click
+            _ = @entry_anti_sense.text
+            e _
+          end
+          if respond_to? :gdk_selection_clipboard
+            @clipboard = widget.get_clipboard(gdk_selection_clipboard)
+            @clipboard.text = _
+            @clipboard.request_text { |clipboard, text, data|
+              # p text # zb label.set_text(text)
+            }
+            @entry_anti_sense.paste_clipboard
+          end
+        end
+      }
+      hbox_with_entry_sense_and_image.add(@eventbox)
+    end
+    @grid.left(hbox_with_entry_sense_and_image)
+    @grid.right(@entry_anti_sense)
+    @grid.left(@box_with_small_buttons)
+    @grid.right(@button_reset)
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                                          (create tag)
+  # ========================================================================= #
+  def create_skeleton
+    create_the_boxes
+    create_the_main_window
+    create_the_entries
+    create_the_buttons # Must come before the main table
+    create_the_grid
+    create_and_add_menu if use_gtk3?
+  end
+
+  # ========================================================================= #
+  # === run                                                         (run tag)
+  # ========================================================================= #
+  def run
+    if use_gtk3?
+      require 'gtk_paradise/requires/require_the_base_module.rb'
+      # extend ::Gtk::BaseModule
+    end
+    create_skeleton
+    # if use_gtk3?
+    #   @outer_vbox.minimal(@menu_bar,   5) # Keep the menu bar small.
+    # end
+    @outer_vbox.minimal(hsep)
+    text_on_top = text(TITLE)
+    text_on_top.align_to_the_left
+    @outer_vbox.minimal(text_on_top)
+
+    # ======================================================================= #
+    # === Handle libui first
+    # ======================================================================= #
+    if is_libui_in_use?
+    elsif is_gtk_in_use?
+    end
+
+    populate_the_grid
+    @outer_vbox.maximal(@grid, 5)
+    @main_window.add(@outer_vbox)
+    @main_window.try_to_add_default_CSS_rules
+    @main_window.intelligent_exit
+    @main_window.show_all
+    connect_skeleton
+    set_use_this_font(USE_THIS_FONT) if use_gtk3?
+    infer_the_size_automatically
+    if use_gtk3?
+      require 'gtk_paradise/run'
+      _ = @main_window
+      r = ::Gtk.run
+      r << _
+      r.background_colour(:linen)
+      r.automatic_size_then_automatic_title
+      r.top_left_then_run
+    else
+      run_main
+    end
+  end
+
+  # ========================================================================= #
+  # === handle_sense
+  #
+  # You can send it an event, or a string.
+  # ========================================================================= #
+  def handle_sense(event)
+    old_text = @entry_sense.text?.dup # stores old text
+    # ======================================================================= #
+    # Store as upcased input:
+    # ======================================================================= #
+    if use_gtk?
+      if event.class == ::Gdk::EventKey
+        event = ::Gdk::Keyval.to_name(event.keyval).upcase
+      else
+        event = event.upcase
+      end
+      case old_text
+      when 'A' then event = 'A'
+      when 'T' then event = 'T'
+      when 'C' then event = 'C'
+      when 'G' then event = 'G'
+      else # do nothing 
+      end
+    else
+      event = event.dup if event.frozen?
+      event.upcase!
+    end
+    @entry_sense.set_text(
+      "#{old_text}#{event}"
+    )
+    synchronize_anti_sense
+  end
+
+end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  Bioroebe::GUI::AntiSenseStrand.new(ARGV)   
+end

data/lib/bioroebe/java/README.md

@@ -0,0 +1,6 @@
+This directory may contain some java code, but do not expect
+bioroebe to ever be fully written in Java.
+
+To compile it anew, do:
+
+  run bioroebe/AllInOne.java