bioroebe 0.10.80 → 0.12.24

data/lib/bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb

@@ -0,0 +1,94 @@
+#!/usr/bin/ruby -w
+# Encoding: UTF-8
+# frozen_string_literal: true
+# =========================================================================== #
+# === Bioroebe::GUI::AminoacidCompositionModule
+#
+# Usage example:
+#
+#   Alignment.new(ARGV)
+#
+# =========================================================================== #
+# require 'bioroebe/gui/shared_code/aminoacid_composition/aminoacid_composition_module.rb'
+# include Bioroebe::GUI::AminoacidCompositionModule
+# =========================================================================== #
+module Bioroebe
+
+module GUI
+
+module AminoacidCompositionModule # === Bioroebe::GUI::AminoacidCompositionModule
+
+  require 'colours'
+  require 'bioroebe/sequence/alignment.rb'
+
+  # ========================================================================= #
+  # === TITLE
+  # ========================================================================= #
+  TITLE = 'Aminoacid Composition'
+
+  # ========================================================================= #
+  # === 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
+
+  # ========================================================================= #
+  # === FILE_MOLECULAR_WEIGHT
+  # ========================================================================= #
+  FILE_MOLECULAR_WEIGHT = Bioroebe.file_molecular_weight
+
+  # ========================================================================= #
+  # === calculated_weight?
+  #
+  # This method will calculate the weight.
+  # ========================================================================= #
+  def calculated_weight?(i)
+    dataset = YAML.load_file(FILE_MOLECULAR_WEIGHT)
+    weight = 0
+    if i.is_a?(String) and !i.empty?
+      chars = i.chars.sort
+      chars.each {|this_char|
+        value = dataset[this_char]
+        weight += value if value
+      }
+    end
+    # ======================================================================= #
+    # Must deduct water too.
+    # ======================================================================= #
+    weight -= (18.0 * (i.size - 1))
+    return weight.round(2)
+  end
+
+  # ========================================================================= #
+  # === filter_away_invalid_aminoacids
+  # ========================================================================= #
+  def filter_away_invalid_aminoacids(i)
+    ::Bioroebe.filter_away_invalid_aminoacids(i)
+  end
+
+  # ========================================================================= #
+  # === return_how_many_aminoacids_are_in_the_sequence
+  # ========================================================================= #
+  def return_how_many_aminoacids_are_in_the_sequence(
+      i = @entry_user_input
+    )
+    return 'This sequence has '+i.text?.to_s.size.to_s+' aminoacids.'
+  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();
+  }
+
+}