bioroebe 0.10.80

data/lib/bioroebe/java/bioroebe/AllInOne.java

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+package bioroebe;
+import bioroebe.*;
+
+/*
+ * This aggregate-file will contain code for the Bioroebe project,
+ * and Java bindings to it.
+ */
+
+/*package bioroebe;*/
+
+import java.util.Scanner; /* <- This belongs to class ReadUserInput */
+
+/*
+ * Next add time-related code.
+ */
+import java.time.format.DateTimeFormatter;  
+import java.time.LocalDateTime;
+
+class Cat extends Base { // cat tag
+
+  private String file_path = null;
+
+  public void cat_this_file(String file_path) {
+    e("HI THERE "+file_path);
+  }
+
+  /* The constructer for Cat */
+  public Cat(String file_path) {
+    cat_this_file(file_path);
+  }
+
+}
+
+public class AllInOne extends Base {
+
+  /*
+   * show_intro()
+   */
+  public static void show_intro() {
+    egreen(
+      "Welcome to the java-implementation of Bioroebe! \n\n"+
+      "Press 'q' or 'quit' to exit.\n"
+    );
+  }
+
+  /*
+   * handle_this_input
+   */
+  public void handle_this_input(String i) {
+    System.out.println("The input is: " + i);
+  }
+
+  /*
+   * to_rna()
+   *
+   * This method will convert all Thymines (T) into Uracile (U).
+   *
+   * To test it, try:
+   *
+   *   for (String i: args) {
+   *     e(to_rna(i));
+   *   }
+   *
+   */
+  public static String to_rna(String i) {
+    i = i.toUpperCase();
+    return i.replace("T","U");
+  }
+  /*
+   * do_read_user_input()
+   */
+  public static void do_read_user_input() {
+    AllInOne x = new AllInOne();
+        
+    Scanner user_input = new Scanner(System.in); // Create a Scanner object
+
+    /* Get new user input in a loop. */
+    while(true) {
+      show_intro();
+      System.out.println("Enter your name:");
+      String name = user_input.nextLine();       // Read the user input
+      name = name.trim();
+      /* Exit on q */
+      if (name.matches("q|quit|break"))
+      {
+        break;
+      }
+      else {
+        x.handle_this_input(name); /* Delegate towards class ReadUserInput here. */
+      }
+    }
+  }
+
+  /*
+   * show_the_current_time()
+   *
+   * This method would return a String such as:
+   *
+   *   04.03.2020, 21:14:13
+   *
+   */
+  public static void show_the_current_time() {
+
+     DateTimeFormatter dtf = DateTimeFormatter.ofPattern(
+       "dd.MM.yyyy, HH:mm:ss"
+     );  
+     LocalDateTime now = LocalDateTime.now();  
+     e(dtf.format(now));  
+  }
+  /*
+   * cliner()
+   */
+  public static void cliner() {
+    e("==============================================================");
+  }
+  public static void main(String[] args) { /* main tag */
+
+    e("Next running the command "+green("`ls`")+":");
+    Esystem.esystem("ls"); /* <- For sys-commands. */
+
+    /* Show the general intro for this class next: */
+    show_intro();
+    show_the_current_time();
+    Codons.display_start_codons();
+
+    /*
+     * The following text is red.
+     */
+    e(red("This text is red!"));
+
+
+    /*
+     * Testing bisulfite treatment next.
+     */
+    cliner();
+    e(
+      "Next testing the method ToplevelMethods.bisulfite_treatment()"
+    );
+    e(ToplevelMethods.bisulfite_treatment("ATG"));
+    cliner();
+
+    e("Next testing for 123A to remove all numbers:\n");
+    e("    123A");
+    String result = new RemoveNumbers().remove_numbers("123A");
+    e("       "+result);
+    cliner();
+
+    e(
+      "\nNext testing: "+
+      green(
+        "PartnerNucleotide().partner_nucleotide(\"A\")"
+      )
+    );
+
+    new PartnerNucleotide().partner_nucleotide("A"); /* Will return "T" */
+    cliner();
+
+    new GenerateRandomDnaSequence(20);
+
+    RemoveFile.remove_file("/Depot/j/test.md");
+
+    e("Is OTTO a Palindrome? "+ 
+      String.valueOf(
+        IsPalindrome.isPalindrome("OTTO")
+      )
+    );
+
+    e("Is ATGGTA a Palindrome? "+ 
+      String.valueOf(
+        IsPalindrome.isPalindrome("ATGGTA")
+      )
+    );
+
+    cliner();
+    e();
+    e("Next we will test SanitizeNucleotideSequence.sanitize_nucleotide_sequence()");
+    e();
+    
+    e(
+      SanitizeNucleotideSequence.sanitize_nucleotide_sequence(
+        "1 ATCCG\n30 TTACG\n50 AAATTTG"
+      )
+    );
+    e();
+
+    e("Next testing ToCamelcase.to_camelcase('foo_bar'):");
+    e(
+      ToCamelcase.to_camelcase("foo_bar")
+    );
+    e();
+
+    e("Next testing BisulfiteTreatment.bisulfite_treatment('ATGCCCCCCCC'):");
+    e(
+      BisulfiteTreatment.bisulfite_treatment("ATGCCCCCCCC")
+    );
+    e();
+
+
+/*
+    e("Next testing class Sequence.");
+    Sequence s = new Sequence("ATCGT");
+    e("The sequence is: "+s.return_string());
+*/
+/*
+new BaseFrame();
+*/
+  }
+
+}
+
+
+// java ToRNA AGATGCAAAAAGACACTACACAGTCACCCCCCCCCAaaatgcCTAGCATCACA
+
+// pwdjava; cd bioroebe; javac read_user_input.java

data/lib/bioroebe/java/bioroebe/Base.java

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+package bioroebe;
+import bioroebe.*;
+
+/*
+ * The Base class defines some constants, in particular in regards
+ * to colours and console-output.
+ */
+public abstract class Base {
+
+  static boolean are_we_on_windows = System.getProperty("os.name").toLowerCase().
+                                     startsWith("windows");
+
+  /*
+   * e()                                                        (e tag)
+   *
+   * method for printing a line.
+   *
+   */
+  public static void e(String i) {
+    System.out.println(i);
+  }
+
+  public static void e() {
+    System.out.println();
+  }
+
+  public static void e(int i) {
+    System.out.println(i);
+  }
+
+  /*
+   * Determine whether the underlying OS is Windows
+   * or whether it is not.
+   */
+  public static boolean on_windows() {
+    return are_we_on_windows;
+  }
+
+  /*
+   * Define some colour-related constants next.
+   */
+
+  public static final String ANSI_RESET  = "\u001B[0m";  // ANSI_RESET
+  public static final String ANSI_BLACK  = "\u001B[30m"; // ANSI_BLACK
+  public static final String ANSI_RED    = "\u001B[31m"; // ANSI_RED
+  public static final String ANSI_GREEN  = "\u001B[32m"; // ANSI_GREEN
+  public static final String ANSI_YELLOW = "\u001B[33m"; // ANSI_YELLOW
+  public static final String ANSI_BLUE   = "\u001B[34m"; // ANSI_BLUE
+  public static final String ANSI_PURPLE = "\u001B[35m"; // ANSI_PURPLE
+  public static final String ANSI_CYAN   = "\u001B[36m"; // ANSI_CYAN
+  public static final String ANSI_WHITE  = "\u001B[37m"; // ANSI_WHITE
+
+  /*
+   * Use a newline.
+   */
+  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)
+   */
+  public static String green(String i) {
+    return ANSI_GREEN+i+ANSI_WHITE;
+  }
+  /*
+   * The colour yellow.
+   */
+  public static String yellow(String i) {
+    return ANSI_YELLOW+i+ANSI_WHITE;
+  }
+  /*
+   * The colour blue.
+   */
+  public static String blue(String i) {
+    return ANSI_BLUE+i+ANSI_WHITE;
+  }
+  /*
+   * echo green output.
+   */
+  public static void egreen(String i) {
+    e(green(i));
+  }
+  /*
+   * echo yellow output.
+   */
+  public static void eyellow(String i) {
+    e(yellow(i));
+  }
+  /*
+   * echo blue output.
+   */
+  public static void eblue(String i) {
+    e(blue(i));
+  }
+
+}

data/lib/bioroebe/java/bioroebe/BisulfiteTreatment.java

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+package bioroebe;
+
+/*
+ * class BisulfiteTreatment
+ *
+ */
+class BisulfiteTreatment extends Base {
+
+  /*
+   * === BisulfiteTreatment.bisulfite_treatment()
+   *
+   * Simply convert all C into U.
+   *
+   * Usage example:
+   *
+   *   BisulfiteTreatment.bisulfite_treatment("ATGCCCCCCCC");
+   *
+   */
+  public static String bisulfite_treatment(String i) {
+    return i.replace("C", "U");
+  }
+
+}

data/lib/bioroebe/java/bioroebe/Codons.java

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+package bioroebe;
+
+/*
+ * class Codons
+ *
+ * This class will include codon-related code.
+ *
+ */
+class Codons extends Base {
+
+  /* Designate the main start codon to use. */
+  public static String start_codon = "ATG";
+
+  /* new Codons.display_start_codons() */
+  public static void display_start_codons() {
+    e(start_codon);
+  }
+  public static String return_start_codon() {
+    return start_codon;
+  }
+
+}

data/lib/bioroebe/java/bioroebe/Esystem.java

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+package bioroebe;
+import java.io.*;
+
+/*
+ * This class can run esystem() aka run a certain command.
+ */
+public class Esystem extends Base {
+
+  /*
+   * Example:
+   *
+   *   Esystem.esystem("ls");
+   *
+   */
+  public static void esystem(String command) {
+
+    e(command);
+
+    try {
+      Process process = Runtime.getRuntime().exec(command);
+
+      BufferedReader reader = new BufferedReader(
+                                new InputStreamReader(process.getInputStream())
+                              );
+      String line;
+      while ((line = reader.readLine()) != null) {
+          System.out.println(line);
+      }
+      reader.close();
+   
+    } catch (IOException error) {
+      error.printStackTrace();
+    }
+  }
+
+  public static void main(String[] args) {
+
+    // deal with OutputStream to send inputs
+    /*process.getOutputStream();*/
+    // deal with InputStream to get ordinary outputs
+    /*process.getInputStream();*/
+    // deal with ErrorStream to get error outputs
+    /*process.getErrorStream();*/
+
+  }
+
+}

data/lib/bioroebe/java/bioroebe/GUI/BaseFrame.java

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+package bioroebe;
+
+import javax.swing.*;
+import java.awt.*;
+
+public class BaseFrame {
+
+  public static void button_is_palindrome_is_clicked() {
+    e("The Palindrome button was clicked.");
+    e(
+      IsPalindrome.isPalindrome("ATTA")
+    );
+  }
+
+  public static void main(String[] args) {
+
+    // Usually you will require both swing and awt packages
+    // even if you are working with just swings.
+
+    // Creating the Frame
+    JFrame frame = new JFrame("Chat Frame");
+    frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
+    frame.setSize(400, 400);
+
+    //Creating the MenuBar and adding components
+    JMenuBar mb = new JMenuBar();
+    JMenu m1 = new JMenu("FILE");
+    JMenu m2 = new JMenu("Help");
+    mb.add(m1);
+    mb.add(m2);
+
+    /* The open functionality: */
+    JMenuItem menu_item1 = new JMenuItem("Open");
+
+    /* The save-as functionality: */
+    JMenuItem menu_item2 = new JMenuItem("Save as");
+    m1.add(menu_item1);
+    m1.add(menu_item2);
+
+    //Creating the panel at bottom and adding components
+    JPanel panel = new JPanel(); // the panel is not visible in output
+    JLabel label = new JLabel("Enter Text");
+    JTextField tf = new JTextField(10); // accepts upto 10 characters
+    JButton send = new JButton("Send");
+    JButton button_is_palindrome = new JButton("Is Palindrome");
+    button_is_palindrome.addActionListener(
+      e -> button_is_palindrome_is_clicked()
+    );
+    JButton reset = new JButton("Reset");
+    panel.add(label); // Components Added using Flow Layout
+    panel.add(tf);
+    panel.add(send);
+    panel.add(button_is_palindrome);
+    panel.add(reset);
+
+    // Text Area at the Center
+    JTextArea ta = new JTextArea();
+
+    //Adding Components to the frame.
+    frame.getContentPane().add(BorderLayout.SOUTH, panel);
+    frame.getContentPane().add(BorderLayout.NORTH, mb);
+    frame.getContentPane().add(BorderLayout.CENTER, ta);
+    frame.setVisible(true);
+  }
+}

data/lib/bioroebe/java/bioroebe/GenerateRandomDnaSequence.java

@@ -0,0 +1,32 @@
+package bioroebe;
+
+import java.util.Random;
+
+/*
+ * This class can generate a random DNA sequence.
+ */
+class GenerateRandomDnaSequence extends Base {
+
+  private String dna_sequence = null;
+
+  /* The constructer for GenerateRandomDnaSequence.
+   *
+   * You input a number, such as 20, and this class
+   * will generate a DNA string of length 20.
+   */
+  public GenerateRandomDnaSequence(int n_characters) {
+
+    String dna_sequence = ""; /* Empty String; it will be returned */
+
+    Random r = new Random();
+
+    String alphabet = "ATCG";
+
+    for (int i = 0; i < n_characters; i++) {
+      dna_sequence += alphabet.charAt(r.nextInt(alphabet.length()));
+    }
+
+    e(dna_sequence);
+  }
+
+}

data/lib/bioroebe/java/bioroebe/IsPalindrome.java

@@ -0,0 +1,18 @@
+package bioroebe;
+
+public class IsPalindrome {
+
+  /*
+   * IsPalindrome.isPalindrome()
+   *
+   */
+  public static boolean isPalindrome(String i) {
+    String reversed = new StringBuffer(i).reverse().toString();
+    return reversed.equals(i); /* Do the comparison here. */
+  }
+
+  public static void main(String[] args) {
+    System.out.println(isPalindrome("OTTO")); /* Will return true. */
+  }
+
+}

data/lib/bioroebe/java/bioroebe/PartnerNucleotide.java

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+package bioroebe;
+
+/*
+ * PartnerNucleotide.partner_nucleotide("A");
+ *
+ * This class will simply yield the corresponding nucleotide.
+ *
+ */
+class PartnerNucleotide extends Base {
+  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;
+    }
+  }
+}

data/lib/bioroebe/java/bioroebe/README.md

@@ -0,0 +1,4 @@
+How to compile this on my home system:
+
+  cd ..
+  run bioroebe/AllInOne.java 

data/lib/bioroebe/java/bioroebe/RemoveFile.java

@@ -0,0 +1,24 @@
+package bioroebe;
+
+import java.io.*; 
+
+/*
+ * RemoveFile.remove_file("A");
+ *
+ * This class can be used to remove a file.
+ *
+ */
+class RemoveFile extends Base {
+  public static void remove_file(String this_file) {
+    File file = new File(this_file);
+
+    /* Check whether the file exists. */
+    if(file.exists() && file.isFile() && file.delete()) {
+      e("The file at `"+this_file+"` was deleted successfully");
+    }
+    else {
+      e("The file at `"+this_file+"` could NOT be deleted");
+    } 
+
+  } 
+}

data/lib/bioroebe/java/bioroebe/RemoveNumbers.java

@@ -0,0 +1,14 @@
+package bioroebe;
+import java.util.Scanner;
+
+/*
+ * RemoveNumbers.remove_numbers("123A");
+ *
+ * This class will simply remove numbers.
+ *
+ */
+class RemoveNumbers extends Base {
+  public static String remove_numbers(String i) {
+    return i.replaceAll("[0-9]","");
+  }
+}

data/lib/bioroebe/java/bioroebe/SanitizeNucleotideSequence.java

@@ -0,0 +1,20 @@
+package bioroebe;
+import bioroebe.*;
+import java.util.Scanner;
+
+/*
+ * SanitizeNucleotideSequence.sanitize_nucleotide_sequence("123A");
+ *
+ * This class will sanitize a DNA sequence..
+ *
+ */
+class SanitizeNucleotideSequence extends Base {
+  /*
+   * sanitize_nucleotide_sequence()
+   */
+  public static String sanitize_nucleotide_sequence(String i) {
+    return i.replace("\n", "").
+             replace("\r", "").
+             replaceAll("\\d", ""); /* The "" is our replacement String. */
+  }
+}

data/lib/bioroebe/java/bioroebe/SaveFile.java

@@ -0,0 +1,44 @@
+package bioroebe;
+
+import java.io.*;
+
+public class SaveFile {
+
+  /*
+   * SaveFile.append_what_into()
+   */
+  public static void append_what_into(
+      String what,
+      String into
+    ) throws IOException
+  {
+    BufferedWriter writer = new BufferedWriter(
+                              new FileWriter(into, true)
+                            );
+    writer.append(what);
+    writer.close();
+  }
+  
+
+  /*
+   *  SaveFile.write_what_into
+   *
+   * This method will simply write the content of the variable `what`
+   * into the file called `into`.
+   */
+  public static void write_what_into(
+      String what,
+      String into
+    ) throws IOException
+  {
+    FileWriter fileWriter = new FileWriter(into);
+    fileWriter.write(what);
+    fileWriter.close();
+  }
+
+/*
+   self.instance_eval { alias save_file       write_what_into } # === Bioroebe.save_file
+     self.instance_eval { alias save_what_where write_what_into } # === Bioroebe.save_what_where
+*/
+
+}