bioroebe 0.10.80 → 0.12.12

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

@@ -0,0 +1,116 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === LibuiParadise::GUI::LibUI::Prototype
+# =========================================================================== #
+module LibuiParadise
+
+module GUI
+
+module LibUI
+
+class Prototype # === LibuiParadise::GUI::LibUI::Prototype
+
+  require 'libui_paradise/extensions/extensions.rb'
+  include LibuiParadise::Extensions
+
+  require 'bioroebe/gui/libui/alignment/alignment.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'A prototype for LibUI'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = 680
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = 520
+
+  # ========================================================================= #
+  # === initialize
+  # ========================================================================= #
+  def initialize(
+      run_already = true
+    )
+    reset
+    run if run_already
+  end
+
+  # ========================================================================= #
+  # === reset                                                     (reset tag)
+  # ========================================================================= #
+  def reset
+    title_width_height(TITLE, WIDTH, HEIGHT)
+  end
+
+  # ========================================================================= #
+  # === create_skeleton                            (create tag, skeleton tag)
+  # ========================================================================= #
+  def create_skeleton
+    # ======================================================================= #
+    # === @window
+    # ======================================================================= #
+    @window = ui_padded_main_window(title?, width?, height?, 0)
+  end
+
+  # ========================================================================= #
+  # === run
+  # ========================================================================= #
+  def run
+    create_skeleton_then_connect_skeleton
+    outer_vbox = padded_vbox
+    # ======================================================================= #
+    # First add the two buttons on top:
+    # ======================================================================= #
+    hbox_on_top = padded_hbox
+    button_refresh = ui_button('Refresh')
+    button_refresh.on_clicked {
+      e 'TODO: Refresh this ... or add any other functionality.'
+    }
+    hbox_on_top.maximal(button_refresh)
+    hbox_on_top.maximal(quit_button)
+    tab = LibuiParadise.tab
+    outer_vbox.maximal(tab)
+    outer_vbox.minimal(hbox_on_top)
+    outer_vbox.add_hsep
+
+    grid = ui_padded_grid
+    #                         widget, left, top, xspan, yspan, hexpand, halign, vexpand, valign
+    grid.ui_grid_append(text('Left'),  0, 0, 1, 1, 0, 0.5, 1, 0)
+    grid.ui_grid_append(text('Right'), 1, 0, 1, 1, 0, 0.5, 1, 0)
+
+    3.times.each {|index| index += 1
+      # ===================================================================== #
+      # left, top, xspan, yspan, hexpand, halign, vexpand, valign
+      #  0,    0,    2,     1,      0,      0,       1,      0
+      # ===================================================================== #
+      grid.ui_grid_append(text(index.to_s), 0, 1+index, 1, 1, 1, 1, 1, 1)
+      label_exam_topic = text(entry.to_s)
+      grid.ui_grid_append(label_exam_topic, 1, 1+index, 1, 1, 1, 1, 1, 1)
+    }
+    outer_vbox.maximal(grid)
+    
+
+    hbox2 = create_hbox
+
+    #alignment = Object.new
+    #alignment.extend(Bioroebe::GUI::LibUI::Alignment)
+    #alignment.reset_then_run
+    #::LibUI.tab_append(tab, 'Page 1', alignment)
+    ::LibUI.tab_append(tab, 'Page 2', hbox2)
+
+    @window.add(outer_vbox)
+    @window.intelligent_exit
+  end
+
+end; end; end; end
+
+if __FILE__ == $PROGRAM_NAME
+  LibuiParadise::GUI::LibUI::Prototype.new  
+end

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

@@ -55,7 +55,7 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
   # ========================================================================= #
   def reset
   end
-    
+
   # ========================================================================= #
   # === create_skeleton                                          (create tag)
   # ========================================================================= #
@@ -125,6 +125,11 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
   def do_generate_a_random_sequence_using_the_value_from_the_proper_entry(
       i = n_aminoacids?
     )
+    i = i.to_i
+    if i > 5_000_000
+      i = 5_000_000
+      set_main_entry(i.to_s)
+    end
     do_generate_a_random_sequence(i)
   end
 
@@ -138,7 +143,11 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
     when nil, :default
       n_aminoacids = GENERATE_N_AMINOACIDS_BY_DEFAULT
     end
-    n_aminoacids = n_aminoacids.to_s
+    n_aminoacids = n_aminoacids.to_i
+    if n_aminoacids > 5_000_000
+      n_aminoacids = 5_000_000
+      set_main_entry(n_aminoacids.to_s)
+    end
     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)
@@ -158,6 +167,13 @@ module RandomSequence # === Bioroebe::GUI::LibUI::RandomSequence
     @entry_use_this_length.text?.to_s
   end
 
+  # ========================================================================= #
+  # === set_main_entry
+  # ========================================================================= #
+  def set_main_entry(i)
+    @entry_use_this_length.set_text(i.to_s)
+  end
+
   # ========================================================================= #
   # === Bioroebe::GUI::LibUI::RandomSequence.run
   # ========================================================================= #

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

@@ -4,6 +4,8 @@
 # =========================================================================== #
 # === Bioroebe::GUI::LibUI::ShowCodonTable
 # =========================================================================== #
+# require 'bioroebe/gui/libui/show_codon_table/show_codon_table.rb'
+# =========================================================================== #
 require 'bioroebe/constants/GUIs.rb'
 
 module Bioroebe

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

@@ -35,11 +35,10 @@ module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
   # === create_skeleton                                          (create tag)
   # ========================================================================= #
   def create_skeleton
-    @entry1 = ui_entry
-    @entry2 = ui_entry
-    @checkbox1 = ui_checkbox
-    @checkbox1.is_active
-    @checkbox2 = ui_checkbox
+    @entry1 = entry
+    @entry2 = entry
+    @checkbox1 = checked_checkbox
+    @checkbox2 = checkbox
   end
 
   # ========================================================================= #
@@ -72,7 +71,7 @@ module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
     small_hbox2 << ui_text('1-to-3 conversion')
     small_hbox2 << @checkbox2
     vbox_with_checkbuttons << small_hbox2
-
+    vbox_with_checkbuttons << quit_button
     bottom_hbox << vbox_with_checkbuttons
     outer_vbox << bottom_hbox
     main_window.child = outer_vbox
@@ -92,6 +91,9 @@ module ThreeToOne # === Bioroebe::GUI::LibUI::ThreeToOne
     else
       new_result = Bioroebe.one_to_three(i.delete('-')).to_s
     end
+    if new_result and new_result.empty?
+      error_msg('No result found. Is it a three-letter aminoacid?')
+    end
     @entry2.set_text(new_result) if new_result and !new_result.empty?
   end; alias do_the_conversion do_trigger_the_conversion # === do_the_conversion
 

data/lib/bioroebe/gui/shared_code/alignment/alignment_module.rb

@@ -0,0 +1,102 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::AlignmentModule
+#
+# Usage example:
+#
+#   Alignment.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/alignment/alignment_module.rb'
+# include Bioroebe::GUI::AlignmentModule
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module AlignmentModule # === Bioroebe::GUI::AlignmentModule
+
+  require 'colours'
+  require 'bioroebe/sequence/alignment.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Alignment'
+
+  # ========================================================================= #
+  # === TEXT_INPUT_THE_SEQUENCES
+  # ========================================================================= #
+  TEXT_INPUT_THE_SEQUENCES = 'Input the sequences that you wish '\
+                             'to compare to one another'
+
+  # ========================================================================= #
+  # === WIDTH
+  # ========================================================================= #
+  WIDTH = '65%'
+
+  # ========================================================================= #
+  # === HEIGHT
+  # ========================================================================= #
+  HEIGHT = '55%'
+
+  # ========================================================================= #
+  # === USE_THIS_FONT
+  # ========================================================================= #
+  USE_THIS_FONT = :dejavu_condensed_22
+
+  # ========================================================================= #
+  # === FONT_FOR_THE_ENTRIES
+  #
+  # The entries must use a mono-spaced font.
+  # ========================================================================= #
+  FONT_FOR_THE_ENTRIES = :hack_20
+
+  # ========================================================================= #
+  # === reset_the_alignment_object
+  # ========================================================================= #
+  def reset_the_alignment_object
+    # ======================================================================= #
+    # === @alignment
+    # ======================================================================= #
+    @alignment = Bioroebe::Alignment.new(nil, :do_not_run_yet)
+  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
+
+  # ========================================================================= #
+  # === return_fill_up_to
+  # ========================================================================= #
+  def return_fill_up_to(i)
+    _ = ''.dup
+    i.times {|counter|
+      counter = (counter+1) % 10
+      _ << counter.to_s
+    }
+    return _
+  end
+
+end; end; end

data/lib/bioroebe/gui/shared_code/levensthein_distance/levensthein_distance_module.rb

@@ -76,20 +76,6 @@ module LevenstheinDistanceModule
     }
   end
 
-  # ========================================================================= #
-  # === padding?
-  # ========================================================================= #
-  def padding?
-    12
-  end
-
-  # ========================================================================= #
-  # === border_size?
-  # ========================================================================= #
-  def border_size?
-    2
-  end
-
   # ========================================================================= #
   # === levensthein_object?
   # ========================================================================= #
@@ -383,8 +369,10 @@ module LevenstheinDistanceModule
       @levensthein_object.edit_distance?
     )
     total_score = @levensthein_object.total_score?.to_s
-    @label_for_the_total_score.set_text(total_score)
-    @label_for_the_total_score.make_bold
+    unless text2.empty?
+      @label_for_the_total_score.set_text(total_score)
+      @label_for_the_total_score.make_bold
+    end
   end; alias do_compare_the_two_sequences do_compare_the_two_strings # === do_compare_the_two_sequences
        alias recalculate_the_score        do_compare_the_two_strings # === recalculate_the_score
 
@@ -399,4 +387,18 @@ module LevenstheinDistanceModule
     return small_label
   end
 
+  # ========================================================================= #
+  # === padding?
+  # ========================================================================= #
+  def padding?
+    12
+  end
+
+  # ========================================================================= #
+  # === border_size?
+  # ========================================================================= #
+  def border_size?
+    4
+  end
+
 end; end; end

data/lib/bioroebe/gui/shared_code/protein_to_DNA/protein_to_DNA_module.rb

@@ -143,13 +143,6 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     end
   end
 
-  # ========================================================================= #
-  # === left_buffer?
-  # ========================================================================= #
-  def left_buffer?
-    @dataset[:left_buffer]
-  end; alias left? left_buffer? # === left?
-
   # ========================================================================= #
   # === right_buffer?
   # ========================================================================= #
@@ -164,6 +157,20 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     @dataset[:left_buffer].set_text(i.to_s)
   end
 
+  # ========================================================================= #
+  # === aminoacid_sequence?
+  # ========================================================================= #
+  def aminoacid_sequence?
+    left_buffer?.to_s
+  end
+
+  # ========================================================================= #
+  # === left_buffer?
+  # ========================================================================= #
+  def left_buffer?
+    @dataset[:left_buffer]
+  end; alias left? left_buffer? # === left?
+
   # ========================================================================= #
   # === do_determine_the_backtrack_sequence                           (click tag)
   #
@@ -182,11 +189,4 @@ module ProteinToDNAModule # === Bioroebe::GUI::ProteinToDNAModule
     right_buffer?.set_text(text_for_right_hand_side)
   end; alias do_determine_the_DNA_sequence do_determine_the_backtrack_sequence # === do_determine_the_DNA_sequence
 
-  # ========================================================================= #
-  # === aminoacid_sequence?
-  # ========================================================================= #
-  def aminoacid_sequence?
-    left_buffer?.to_s
-  end
-
 end; end; end

data/lib/bioroebe/gui/swing/three_to_one/ThreeToOne.java

@@ -0,0 +1,141 @@
+/* package ThreeToOne; */
+import javax.swing.*;
+import java.awt.*;
+import java.awt.event.*;
+import java.awt.Dimension;
+import java.awt.event.KeyAdapter;
+import java.awt.event.KeyEvent;
+
+import java.util.Random;
+import javax.swing.border.EmptyBorder;
+
+import java.util.*;
+import java.util.HashMap;
+import java.util.Map;
+
+public class ThreeToOne {
+
+  private static final String TITLE = "Three To One - Aminoacid Code Converter";
+
+  /*
+   * HASH_THREE_TO_ONE
+   */
+/*
+  Hashtable<String, String> HASH_THREE_TO_ONE = new Hashtable<String, String>();
+*/
+
+/*  HASH_THREE_TO_ONE.put("Ala", "A");
+*/
+
+
+  public Hashtable<String, String> hash = new Hashtable<>(); /* Only have to specify the types once */
+  
+
+  public static JTextField entry1,
+                           entry2;
+  /*
+   * Main constructor (def initialize)
+   */
+  public ThreeToOne() {
+    run();
+  }
+  void initialize_the_main_hash() {
+    hash.put("Ala", "A");
+  }
+  /*
+   * run()
+   */
+  void run() {
+
+    JFrame frame = new JFrame(TITLE);
+
+    frame.setLayout(new GridLayout(5, 2)); /* (int rows, int cols) */
+    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+
+    JLabel label_title = new JLabel("Input Sequence");
+    label_title.setFont(new Font("Serif", Font.PLAIN, 30)); /* Set a new font size */
+
+    frame.add(label_title);
+    frame.add(new JLabel(""));
+
+    /* Input Sequence */
+    entry1 = new JTextField(30);
+    entry1.setFont(new Font("Serif", Font.PLAIN, 20));
+    entry1.setMargin(new Insets(4, 4, 4, 4));
+    entry1.setHorizontalAlignment(JTextField.CENTER);
+    entry1.setFocusable(true);
+    frame.add(entry1);
+    frame.add(new JLabel(""));
+
+    /* Fahrenheit */
+    entry2 = new JTextField(30);
+    entry2.setFont(new Font("Serif", Font.PLAIN, 20));
+    entry2.setMargin(new Insets(4, 4, 4, 4));
+    entry2.setHorizontalAlignment(JTextField.CENTER);
+    entry2.setFocusable(true);
+    frame.add(entry2);
+    frame.add(new JLabel(""));
+    
+    JButton convert_button = new JButton("Convert");
+    
+    frame.add(convert_button);
+    frame.add(return_quit_button());
+
+    frame.setSize(1200, 500);
+    frame.setVisible(true);
+
+    initialize_the_main_hash();
+
+    convert_button.setMnemonic('C');
+    convert_button.setBounds(10, 80, 80, 25); /* int x-coordinate, int y-coordinate, int width, int height */
+    convert_button.addActionListener(
+      e -> do_the_conversion()
+    );
+
+  }
+  /*
+   * return_quit_button()
+   */
+  JButton return_quit_button() {
+    JButton quit_button = new JButton("Quit");
+    quit_button.addActionListener(new CloseListener());
+    quit_button.setMnemonic('Q');
+    return quit_button;
+  }
+  private class CloseListener implements ActionListener {
+    @Override
+    public void actionPerformed(ActionEvent e) {
+      System.exit(0);
+    }
+  }
+
+  /*
+   * do_the_conversion()
+   */
+  void do_the_conversion() {
+    if (entry1.getText().isEmpty()) {
+      en("No text to check.");
+    }
+    else {
+      String target_key = entry1.getText();
+
+      if (hash.containsKey(target_key)) {
+        String result = hash.get(target_key);
+        entry2.setText(result);
+      };
+    }
+  }
+
+  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) {
+    ThreeToOne x = new ThreeToOne();
+  }
+
+}

data/lib/bioroebe/java/README.md

@@ -4,3 +4,7 @@ bioroebe to ever be fully written in Java.
 To compile it anew, do:
 
   run bioroebe/AllInOne.java 
+
+Since as of September 2022 it is easier to run:
+
+  bioroebe --create-jar

data/lib/bioroebe/java/bioroebe/Sequence.java

@@ -10,14 +10,38 @@ import java.io.*;
  */
 public class Sequence extends Base {
 
+  private static final boolean SHALL_WE_UPCASE = true;
   private static String sequence = "";
  
   public static void main(String[] args) {
     sequence = String.join("", args);
   }
+  /*
+   *
+   * === n_uracil?
+   *
+   * Report how many Uracil can be found in the given String. This is more
+   *  of an ad-hoc method, though.
+   */
+  int n_uracil() {
+    String modified_sequence = sequence.
+                               toUpperCase().
+                               replace("T","U").
+                               count('U');
+    return modified_sequence.
+           chars().
+           filter(ch -> ch == 'U').
+           count(); /* This is .count('U') */
+  }
 
   /*
-   * return_sequence()
+   * === shall_we_upcase()
+   */
+  boolean shall_we_upcase() {
+    return SHALL_WE_UPCASE;
+  }
+  /*
+   * Sequence.return_sequence()
    *
    * Will return the sequence of our class Sequence instance.
    */

data/lib/bioroebe/java/bioroebe/{Base.java → src/main/java/bioroebe/Base.java}

@@ -1,11 +1,14 @@
 package bioroebe;
+
 import bioroebe.*;
 
 /*
  * The Base class defines some constants, in particular in regards
  * to colours and console-output.
  */
-public abstract class Base {
+/*public abstract class Base {*/
+
+public class Base {
 
   static boolean are_we_on_windows = System.getProperty("os.name").toLowerCase().
                                      startsWith("windows");
@@ -56,12 +59,14 @@ public abstract class Base {
   public static void newline() {
     System.out.println();
   }
+
   /*
    * The colour red.
    */
   public static String red(String i) {
     return ANSI_RED+i+ANSI_WHITE;
   }
+
   /*
    * The colour green.                                              (green tag)
    */
@@ -99,4 +104,12 @@ public abstract class Base {
     e(blue(i));
   }
 
-}
+  /*
+   * The main method here is only used for testing purposes.
+   */
+  public static void main(String[] args) {
+    Base x = new Base();
+    x.eblue("WTF");
+  }
+  
+}