bioroebe 0.10.80 → 0.12.24

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

@@ -107,7 +107,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     scrolled_window_right.clear_background
     scrolled_window_right.width_height(300, 300)
     scrolled_window_right.bblack1
-    scrolled_window_right.css_class('mar2px')
+    scrolled_window_right.mar2px
     # ======================================================================= #
     # === scrolled_window_left
     # ======================================================================= #
@@ -115,7 +115,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     scrolled_window_left.clear_background
     scrolled_window_left.width_height(300, 300)
     scrolled_window_left.bblack1
-    scrolled_window_left.css_class('mar2px')
+    scrolled_window_left.mar2px
     top_hpaned = gtk_hpaned(
       scrolled_window_left,
       scrolled_window_right
@@ -126,22 +126,6 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     @dataset[:top_hbox] = top_hpaned
   end
 
-  # ========================================================================= #
-  # === connect_skeleton                                        (connect tag)
-  # ========================================================================= #
-  def connect_skeleton
-    abort_on_exception
-    @main_vbox.maximal(@dataset[:top_hbox], 4)
-    @main_vbox.maximal(@middle_bar)
-    button_box = button_box(
-      @dataset[:backtrack_button],
-      @dataset[:quit_button]
-    )
-    button_box.vertical_layout
-    @main_vbox.minimal(button_box)
-    add(@main_vbox)
-  end
-
   # ========================================================================= #
   # === create_left_buffer
   # ========================================================================= #
@@ -161,6 +145,22 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     super()
   end
 
+  # ========================================================================= #
+  # === connect_skeleton                                        (connect tag)
+  # ========================================================================= #
+  def connect_skeleton
+    abort_on_exception
+    @main_vbox.maximal(@dataset[:top_hbox], 4)
+    @main_vbox.maximal(@middle_bar)
+    button_box = button_box(
+      @dataset[:backtrack_button],
+      @dataset[:quit_button]
+    )
+    button_box.vertical_layout
+    @main_vbox.minimal(button_box)
+    add(@main_vbox)
+  end
+
   # ========================================================================= #
   # === Bioroebe::GUI::Gtk::ProteinToDNA.run
   # ========================================================================= #
@@ -171,8 +171,7 @@ class ProteinToDNA < ::Gtk::Box # === Bioroebe::GUI::Gtk::ProteinToDNA
     _ = ::Bioroebe::GUI::Gtk::ProteinToDNA.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end; self.instance_eval { alias run_gtk3_widget run } # === Bioroebe::GUI::Gtk::ProteinToDNA.run_gtk3_widget
 
 end; end; end; end

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

@@ -43,12 +43,12 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
   # ========================================================================= #
   # === WIDTH
   # ========================================================================= #
-  WIDTH  = 900
+  WIDTH = '45% or minimum 1200px'
 
   # ========================================================================= #
   # === HEIGHT
   # ========================================================================= #
-  HEIGHT = 720
+  HEIGHT = '45% or minimum 980px'
 
   # ========================================================================= #
   # === USE_THIS_HEADER
@@ -478,8 +478,20 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
     create_the_entries
   end
 
+  # ========================================================================= #
+  # === handle_CSS
+  # ========================================================================= #
+  def handle_CSS
+    use_gtk_paradise_project_css_file
+    use_project_css_file
+    apply_the_CSS
+  end
+
   # ========================================================================= #
   # === do_generate_a_random_sequence
+  #
+  # This is the method that will be run whenever a new random aminoacid
+  # sequence is to be generated.
   # ========================================================================= #
   def do_generate_a_random_sequence(
       n_aminoacids = :default
@@ -521,18 +533,14 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
     # list-store.
     # ======================================================================= #
     array = array1.zip(array2) # Zip it up with 0-values here.
+    # ======================================================================= #
+    # Next, populate the liststore with the new data - since as of July
+    # 2022 we will sort it based on most aminoacids though:
+    # ======================================================================= #
+    array = array.sort_by {|a, b| b }.reverse # This sorts by highest first.
     ::Gtk.populate_this_liststore(@list_store, array)
   end
 
-  # ========================================================================= #
-  # === handle_CSS
-  # ========================================================================= #
-  def handle_CSS
-    use_gtk_paradise_project_css_file
-    use_project_css_file
-    apply_the_CSS
-  end
-
   # ========================================================================= #
   # === run
   # ========================================================================= #
@@ -553,10 +561,9 @@ class RandomSequence < ::Gtk::Box # === Bioroebe::GUI::Gtk::RandomSequence
     _ = ::Bioroebe::GUI::Gtk::RandomSequence.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
     r.background_colour :white
     r.easy_exit
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end; self.instance_eval { alias run start_gui_application } # === RandomSequence.run
 
 end; end; end; end

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

@@ -297,8 +297,7 @@ class RestrictionEnzymes < ::Gtk::Box # === Bioroebe::GUI::Gtk::RestrictionEnzym
     r.add_shortcut(3, 'focus_entry(3)', :alt)
     r.add_shortcut(4, 'focus_entry(4)', :alt)
     r.background_colour :whitesmoke
-    r.infer_the_size
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end; self.instance_eval { alias start_gui_application run } # === RestrictionEnzymesModule.start_gui_application
        self.instance_eval { alias run_gtk3_widget       run } # === RestrictionEnzymesModule.run_gtk3_widget
 

data/lib/bioroebe/gui/gtk3/show_codon_table/misc.rb

@@ -12,16 +12,11 @@ module GUI
 
 module Gtk
 
-class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
+class ShowCodonTable < ::Gtk::BaseModuleBox # === Bioroebe::GUI::Gtk::ShowCodonTable
 
   require 'bioroebe/gui/shared_code/show_codon_table/show_codon_table_module.rb'
   include Bioroebe::GUI::ShowCodonTableModule
 
-  # ========================================================================= #
-  # === NAMESPACE
-  # ========================================================================= #
-  NAMESPACE = inspect
-
   # ========================================================================= #
   # === USE_THIS_FONT
   #
@@ -35,10 +30,11 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
   def reset
     reset_the_internal_variables
     reset_the_shared_module
+    infer_the_namespace
     # ======================================================================= #
     # === @configuration
     # ======================================================================= #
-    @configuration = [true, __dir__, NAMESPACE]
+    @configuration = [true, __dir__, namespace?]
     set_use_this_font(USE_THIS_FONT)
     handle_CSS
     infer_the_size_automatically
@@ -384,20 +380,6 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
     @scrolled_window.use_this_font = smaller_font?
   end
 
-  # ========================================================================= #
-  # === Bioroebe::GUI::Gtk::ShowCodonTable.run
-  # ========================================================================= #
-  def self.run(
-      i = ARGV
-    )
-    require 'gtk_paradise/run'
-    _ = ::Bioroebe::GUI::Gtk::ShowCodonTable.new(i)
-    r = ::Gtk.run
-    r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
-  end
-
   # ========================================================================= #
   # === create_the_combo_box_containing_the_available_codon_tables
   #
@@ -450,7 +432,7 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
   # This is the "title" bar, the main header, on top of the widget.
   # ========================================================================= #
   def create_the_title_bar
-    hbox = gtk_hbox
+    hbox = create_hbox
     # ======================================================================= #
     # For the following gtk-label, always keep a leading ' '.
     # ======================================================================= #
@@ -537,6 +519,14 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
   def handle_CSS
     use_gtk_paradise_project_css_file
     use_project_css_file
+    more_CSS '
+tooltip {
+  padding:      25px;
+  border-width: 3px;
+  border-style: dotted;
+  border-color: orange;
+}
+'
     apply_the_CSS
   end
 
@@ -553,4 +543,89 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
     end
   end
 
+  # ========================================================================= #
+  # === create_the_box_containing_the_label_and_the_combobox
+  # ========================================================================= #
+  def create_the_box_containing_the_label_and_the_combobox
+    # ======================================================================= #
+    # === @label_and_combo_box
+    # ======================================================================= #
+    @label_and_combo_box = gtk_vbox
+    @label_and_combo_box.minimal(
+      left_aligned_label(
+        ' Select the codon table (default: <b>eukaryotes</b>)'
+      ), 8
+    )
+    hbox = gtk_hbox
+    hbox.minimal(@combo_box_containing_the_registered_codon_tables, 2)
+    @label_and_combo_box.minimal(
+      hbox, 2
+    )
+  end
+
+  # ========================================================================= #
+  # === return_widget_containing_the_toggle_buttons
+  #
+  # These are the four "toggle" buttons on the right side of the widget.
+  # ========================================================================= #
+  def return_widget_containing_the_toggle_buttons
+    hbox = create_hbox
+    hbox.pad8px
+    @button1 = create_bold_button('T')
+    @button1.foreground_colour = :royalblue
+    @button1.bblack1
+    @button1.on_clicked {
+      change_label(@button1)
+    }
+    @button2 = create_bold_button('T')
+    @button2.foreground_colour = :royalblue
+    @button2.bblack1
+    @button2.on_clicked {
+      change_label(@button2)
+    }
+    @button3 = create_bold_button('T')
+    @button3.foreground_colour = :royalblue
+    @button3.bblack1
+    @button3.on_clicked {
+      change_label(@button3)
+    }
+    # ======================================================================= #
+    # Next comes the button that will also show '*'.
+    # ======================================================================= #
+    @button4 = create_bold_button('T')
+    @button4.foreground_colour = :crimson
+    @button4.bblack1
+    @button4.set_name('custom_tooltip')
+    @button4.hint =
+      "\nThis button is special in that it will denote "\
+      "the current aminoacid. The other three buttons "\
+      "represent the codon at different positions.\n\n"\
+      "A '<b>*</b>' indicates a stop-codon.\n"
+    # button4.on_clicked {
+    #   change_label(button4)
+    # }
+    bbox = gtk_button_box_spread(
+      @button1,
+      @button2,
+      @button3
+    )
+    hbox.minimal(bbox,                             2)
+    hbox.minimal(gtk_button_box_spread(@button4), 10)
+    return hbox
+  end
+
+  # ========================================================================= #
+  # === Bioroebe::GUI::Gtk::ShowCodonTable.run
+  # ========================================================================= #
+  def self.run(
+      i = ARGV
+    )
+    require 'gtk_paradise/run'
+    _ = ::Bioroebe::GUI::Gtk::ShowCodonTable.new(i)
+    r = ::Gtk.run
+    r << _
+    r.automatic_top_left_then_run
+    r.easy_exit
+  end
+
 end; end; end; end

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

@@ -15,16 +15,13 @@ module GUI
 
 module Gtk
 
-class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable 
+class ShowCodonTable < ::Gtk::BaseModuleBox # === Bioroebe::GUI::Gtk::ShowCodonTable 
 
   require 'bioroebe/gui/gtk3/show_codon_table/misc.rb'
 
   require 'bioroebe/codons/codon_tables.rb'
   require 'bioroebe/constants/GUIs.rb'
 
-  require 'gtk_paradise/requires/require_the_base_module.rb'
-  include ::Gtk::BaseModule
-
   # ========================================================================= #
   # === initialize
   # ========================================================================= #
@@ -42,73 +39,6 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
     run if run_already
   end
 
-  # ========================================================================= #
-  # === return_widget_containing_the_toggle_buttons
-  #
-  # These are the four "toggle" buttons on the right side of the widget.
-  # ========================================================================= #
-  def return_widget_containing_the_toggle_buttons
-    hbox = gtk_hbox
-    hbox.pad8px
-    @button1 = gtk_bold_button('T')
-    @button1.foreground_colour = :royalblue
-    @button1.bblack1
-    @button1.on_clicked {
-      change_label(@button1)
-    }
-    @button2 = gtk_bold_button('T')
-    @button2.foreground_colour = :royalblue
-    @button2.bblack1
-    @button2.on_clicked {
-      change_label(@button2)
-    }
-    @button3 = gtk_bold_button('T')
-    @button3.foreground_colour = :royalblue
-    @button3.bblack1
-    @button3.on_clicked {
-      change_label(@button3)
-    }
-    @button4 = gtk_bold_button('T')
-    @button4.foreground_colour = :crimson
-    @button4.bblack1
-    @button4.hint =
-      "\nThis button is special in that it will denote "\
-      "the current aminoacid. The other three buttons "\
-      "represent the codon at different positions.\n\n"\
-      "A '*' indicates a stop-codon.\n"
-    # button4.on_clicked {
-    #   change_label(button4)
-    # }
-    bbox = gtk_button_box_spread(
-      @button1,
-      @button2,
-      @button3
-    )
-    hbox.minimal(bbox,                             2)
-    hbox.minimal(gtk_button_box_spread(@button4), 10)
-    return hbox
-  end
-
-  # ========================================================================= #
-  # === create_the_box_containing_the_label_and_the_combobox
-  # ========================================================================= #
-  def create_the_box_containing_the_label_and_the_combobox
-    # ======================================================================= #
-    # === @label_and_combo_box
-    # ======================================================================= #
-    @label_and_combo_box = gtk_vbox
-    @label_and_combo_box.minimal(
-      left_aligned_label(
-        ' Select the codon table (default: <b>eukaryotes</b>)'
-      ), 8
-    )
-    hbox = gtk_hbox
-    hbox.minimal(@combo_box_containing_the_registered_codon_tables, 2)
-    @label_and_combo_box.minimal(
-      hbox, 2
-    )
-  end
-
   # ========================================================================= #
   # === create_the_top_vbox
   # ========================================================================= #
@@ -134,7 +64,7 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
     right_vbox.minimal(gtk_horizontal_spacer,                        2)
     right_vbox.minimal(return_widget_containing_the_toggle_buttons, 12)
     _ = drag_it_left_to_right(left_vbox, right_vbox)
-    _.position = @width / 4.5
+    _.position = width? / 4.5
     main_box = can_be_dragged_up_and_down(
       top_box?,
       _
@@ -160,7 +90,7 @@ class ShowCodonTable < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonTable
   # === run                                                         (run tag)
   # ========================================================================= #
   def run
-    create_skeleton_then_connect_skeleton
+    super()
     clear_the_main_hash_before_syncing_the_dataset_onto_the_main_table
   end
 

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

@@ -135,8 +135,7 @@ class ShowCodonUsage < ::Gtk::Box # === Bioroebe::GUI::Gtk::ShowCodonUsage
     _ = ::Bioroebe::GUI::Gtk::ShowCodonUsage.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.middle_then_run
+    r.automatic_middle_then_run
   end
 
 end; end; end; end

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

@@ -196,8 +196,7 @@ class Sizeseq < ::Gtk::Box # === Bioroebe::GUI::Gtk::Sizeseq
     _ = ::Bioroebe::GUI::Gtk::Sizeseq.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
 end; end; end; end

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

@@ -221,8 +221,7 @@ class ThreeToOne < ::Gtk::Box # === Bioroebe::GUI::Gtk::ThreeToOne
     _ = ::Bioroebe::GUI::Gtk::ThreeToOne.new(i)
     r = ::Gtk.run
     r << _
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end
 
   # ========================================================================= #

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

@@ -357,8 +357,7 @@ class WwwFinder < ::Gtk::Box # === Bioroebe::GUI::Gtk::WwwFinder
     r.add_shortcut(3, 'focus_entry(3)', :alt)
     r.add_shortcut(4, 'focus_entry(4)', :alt)
     r.background_colour :white
-    r.automatic_size_then_automatic_title
-    r.top_left_then_run
+    r.automatic_top_left_then_run
   end; self.instance_eval { alias start_gui_application run } # === Bioroebe::GUI::Gtk::WwwFinder.start_gui_application
 
 end; end; end; end

data/lib/bioroebe/gui/javafx/bioroebe/Bioroebe.java

@@ -0,0 +1,104 @@
+package bioroebe;
+
+import javafx.application.*;
+import javafx.stage.*;
+import javafx.scene.*;
+import javafx.scene.layout.*;
+import javafx.scene.control.*;
+import javafx.scene.text.Font;
+import javafx.scene.text.FontWeight;
+
+public class Bioroebe extends Application /* < Application */
+{
+
+   private static final double screen_width  = Screen.getPrimary().getBounds().getWidth();
+   private static final double screen_height = Screen.getPrimary().getBounds().getHeight();
+
+  /*
+   * === TITLE
+   */
+  private static final String TITLE = "The Bioroebe Project";
+
+  /* === WIDTH */
+  private static final double WIDTH = screen_width;
+
+  /* === HEIGHT */
+  private static final double HEIGHT = screen_height;
+
+  public static void e(String i) {
+    System.out.print(i);
+  } 
+
+  public static void en(String i) {
+    System.out.println(i);
+  }
+
+  public static void main(String[] args)
+  {
+    launch(args);
+  }
+  Button button1,
+         button2,
+         button_exit;
+
+  /*
+   * start()
+   */
+  @Override public void start(Stage primaryStage)
+  {
+    // Create the button
+    button1 = new Button();
+    button1.setText("Click me please!");
+    button1.setOnAction(e -> buttonClick());
+    // Add the button to a layout pane
+    BorderPane pane = new BorderPane();
+    
+    HBox hbox2 = new HBox(12);
+    hbox2.getChildren().addAll(button1, new Label("Test"));
+    pane.setCenter(hbox2);
+
+    button2 = new Button();
+    button2.setText("Yet another button!");
+    button2.setOnAction(e -> button2_was_clicked());
+
+    button_exit = new Button("Exit");
+    button_exit.setOnAction(e -> Platform.exit());
+
+    HBox hbox1 = new HBox(8); /* spacing = 8 */
+    hbox1.getChildren().addAll(
+      button2,
+      button_exit
+    );
+    pane.setBottom(hbox1);
+    pane.setStyle("-fx-font-size: 22");
+  
+    /*
+     * Add the layout pane to a scene via the two
+     * defined constants. That pane is the root
+     * node.
+     */
+    Scene scene = new Scene(pane, WIDTH, HEIGHT);
+    
+    // Finalize and show the stage
+    primaryStage.setScene(scene);
+    primaryStage.setTitle(TITLE);
+    primaryStage.show();
+  }
+
+  /* Toggline the button-state here */
+  public void buttonClick()
+  {
+    if (button1.getText() == "Click me please!")
+    {
+      button1.setText("You clicked me!");
+    }
+    else
+    {
+      button1.setText("Click me please!");
+    }
+  }
+  public void button2_was_clicked() {
+    en("I was clicked");
+  }
+  
+}

data/lib/bioroebe/gui/javafx/bioroebe.mf

@@ -0,0 +1 @@
+Main-Class: Bioroebe

data/lib/bioroebe/gui/javafx/module-info.java

@@ -0,0 +1,5 @@
+module bioroebe
+{
+  requires javafx.controls;
+  exports bioroebe;
+}