bioroebe 0.10.80 → 0.11.32

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/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");
+  }
+  
+}

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Codons.java

@@ -0,0 +1,34 @@
+package bioroebe;
+
+/*
+ * class Codons
+ *
+ * This class will include codon-related code.
+ *
+ * It is currently very unfinished, but should ideally
+ * be useable for some toplevel method calls such as:
+ *
+ *   Codons.is_valid_start_codon("UUU") # => true or false
+ *
+ */
+class Codons extends Base {
+
+  /* Designate the main start codon to use. */
+  public static String start_codon = "ATG";
+
+  /*
+   * Codons.display_start_codons()
+   *
+   * This shall simply display all valid start codons.
+   *
+   * We currently miss reporting GTG and another one;
+   * this has to be fixed eventually.
+   */
+  public static void display_start_codons() {
+    e(start_codon);
+  }
+  public static String return_start_codon() {
+    return start_codon;
+  }
+
+}

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/Commandline.java

@@ -0,0 +1,95 @@
+/*
+ * This class will handle commandline-given input.
+ */
+package bioroebe;
+
+public class Commandline {
+
+  /*
+   * Main constructor (def initialize)
+   */
+  String[] commandline_arguments;
+  public Commandline(String[] args) {
+    commandline_arguments = args;
+    run();
+  }
+  /*
+   * show_help()                                                     (help tag)
+   *
+   * show help instructions for this class.
+   */
+  void show_help() {
+    en("The following commandline options are available:");
+    en("");
+    en("  --partner             # complement via partner molecules");
+    en("  --random-dna-sequence # output a random DNA sequence");
+    en("");
+  }
+  /*
+   * run()
+   */
+  void run() {
+    if (commandline_arguments.length > 0) {
+      for (String entry : commandline_arguments) {
+        /* --help */
+        if (entry.matches("help|--help")) {
+          show_help();
+        }
+        /* java bioroebe/Commandline --is-palindrome */
+        else if (entry.matches("is[\s_-]*palindrome|--is_palindrome")) {
+          System.out.println(
+            IsPalindrome.isPalindrome("OTTO")
+          );
+        }
+        /* java bioroebe/Commandline --random-dna-sequence */
+        else if (entry.matches("random-dna-sequence|--random-dna-sequence")) {
+          new GenerateRandomDnaSequence(250);
+        }
+        /* java bioroebe/Commandline --start-codons */
+        else if (entry.matches("start-codons|--start-codons")) {
+          Codons.display_start_codons();
+        }
+        /* java bioroebe/Commandline --esystem */
+        else if (entry.matches("esystem|--esystem")) {
+          Esystem.esystem("ls");
+        }
+        /* java bioroebe/Commandline --bisulfite */
+        else if (entry.matches("bisulfite|--bisulfite")) {
+          en(
+            BisulfiteTreatment.bisulfite_treatment("ATGCCCCCCCC")
+          );
+        }
+        /* java bioroebe/Commandline --remove-numbers */
+        else if (entry.matches("remove-numbers|--remove-numbers")) {
+          en(
+            RemoveNumbers.remove_numbers("123A")
+          );
+        }
+        else if (entry.matches("partner|--partner")) {
+          en(
+            PartnerNucleotide.return_partner_nucleotide("A")
+          );
+        }
+        else {
+          en("Unsure what to do with: "+entry);
+        }
+      }
+    }
+    else {
+      en("Please provide input to this class.");
+    }
+  }
+
+  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) {
+    Commandline x = new Commandline(args);
+  }
+
+}

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

@@ -9,10 +9,16 @@ class GenerateRandomDnaSequence extends Base {
 
   private String dna_sequence = null;
 
-  /* The constructer for GenerateRandomDnaSequence.
+  /*
+   * The constructor for GenerateRandomDnaSequence.
    *
    * You input a number, such as 20, and this class
    * will generate a DNA string of length 20.
+   *
+   * Usage example:
+   *
+   *   new GenerateRandomDnaSequence(250);
+   *
    */
   public GenerateRandomDnaSequence(int n_characters) {
 
@@ -26,7 +32,7 @@ class GenerateRandomDnaSequence extends Base {
       dna_sequence += alphabet.charAt(r.nextInt(alphabet.length()));
     }
 
-    e(dna_sequence);
+    e(dna_sequence); /* And output the DNA sequence here. */
   }
 
 }

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

@@ -1,10 +1,14 @@
 package bioroebe;
 
-public class IsPalindrome {
+public class IsPalindrome extends Base {
 
   /*
    * IsPalindrome.isPalindrome()
    *
+   * Usage example:
+   *
+   *   IsPalindrome.isPalindrome("OTTO")
+   *
    */
   public static boolean isPalindrome(String i) {
     String reversed = new StringBuffer(i).reverse().toString();

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/PartnerNucleotide.java

@@ -0,0 +1,56 @@
+package bioroebe;
+
+import bioroebe.*;
+
+/*
+ * PartnerNucleotide.partner_nucleotide("A");
+ *
+ * This class will simply yield the corresponding nucleotide.
+ *
+ * Usage example:
+ *
+ *   PartnerNucleotide.partner_nucleotide("A");
+ *
+ */
+class PartnerNucleotide extends Base {
+
+  /*
+   * PartnerNucleotide.partner_nucleotide()
+   */
+  public static void partner_nucleotide(String i) {
+    switch(i) {
+      case "A": e("T"); break;
+      case "T": e("A"); break;
+      case "C": e("G"); break;
+      case "G": e("C"); break;
+      default: e("Unhandled input "+i); break;
+    }
+  }
+
+  /*
+   * PartnerNucleotide.return_partner_nucleotide()
+   */
+  public static String return_partner_nucleotide(String i) {
+    switch(i) {
+      case "A": return ("T");
+      case "T": return ("A");
+      case "C": return ("G");
+      case "G": return ("C");
+      default: return ("Unhandled input "+i);
+    }
+  }
+
+  public static void main(String[] args) {
+
+    if (args.length > 0) {
+      for (String string : args) {
+        PartnerNucleotide.partner_nucleotide(string);
+      }
+    }
+    else {
+      System.out.println("Please provide input to this class, a DNA sequence.");
+    }
+
+  }
+
+}

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

@@ -1,6 +1,6 @@
 package bioroebe;
 
-import java.io.*; 
+import java.io.*;
 
 /*
  * RemoveFile.remove_file("A");
@@ -18,7 +18,13 @@ class RemoveFile extends Base {
     }
     else {
       e("The file at `"+this_file+"` could NOT be deleted");
-    } 
+    }
+
+  }
+}
+
+/*
 
-  } 
-}
+  RemoveFile.remove_file("/Depot/j/test.md");
+  
+*/

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

@@ -1,4 +1,5 @@
 package bioroebe;
+
 import java.util.Scanner;
 
 /*

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

@@ -13,13 +13,13 @@ class ToCamelcase extends Base {
    *
    * Usage example:
    *
-   *   ToCamelcase.to_camelcase("foo_bar");
-   *
+   *   ToCamelcase.to_camelcase("foo_bar"); # => "FooBar"
+   
    */
   public static String to_camelcase(String i) {
 
     StringBuilder sb = new StringBuilder();
-    
+
     for( String entry : i.toLowerCase().split("_") )
     {
       sb.append( entry.substring(0,1).toUpperCase() );

data/lib/bioroebe/java/bioroebe/src/main/java/bioroebe/ToRNA.java

@@ -0,0 +1,42 @@
+/* package ToRNA; */
+
+public class ToRNA {
+
+  static String[] commandline_arguments;
+
+  /*
+   * Main constructor (def initialize)
+   */
+  public ToRNA() {
+    run();
+  }
+  /*
+   * run()
+   */
+  void run() {
+    
+    if (commandline_arguments.length > 0) {
+      for (String entry : commandline_arguments) {
+        en(entry);
+      }
+    }
+    else {
+      en("Please provide an input to this method, a DNA sequence.");
+    }
+
+  }
+
+  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) {
+    commandline_arguments = args;
+    ToRNA x = new ToRNA();
+  }
+
+}